| WBIC | Impaired Water ID | Waterbody Name | Counties | Start Mile | End Mile or Acres | Impaired Water Priority | Impaired Water Category | Impaired Water Status | Pollutants | Impairments | DNR Category | Regions |
| 178400 | 336 | Peppermill Creek | Adams | 0 | 1.71 | NA | NPS | Delist | Sediment | Degraded Habitat, Elevated Water Temperature | Category 2 | West Central Region |
| 176300 | 498 | Unnamed Trib To Mason Lake | Adams | 2.7 | 6 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | West Central Region |
| 1179900 | 530 | Wisconsin River | Adams, Columbia, Juneau, Sauk | 138 | 158.68 | Low Priority | Contam. Sediment, Other Factors | 303d Listed | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | South Central Region, West Central Region |
| 1345700 | 534 | Castle Rock Lake | Adams, Juneau | 0 | 12385.6 | Low Priority | Contam. Sediment, PS/NPS Blend | 303d Listed, Deletion | Dioxin, Mercury, PCBs, Total Nitrogen | Contaminated Fish Tissue, Low DO, pH | Category 5A | West Central Region |
| 1377100 | 536 | Petenwell Lake | Adams, Juneau | 0 | 23000.8 | Low Priority | Contam. Sediment, PS/NPS Blend | 303d Listed | Dioxin, Mercury, PCBs, Total Phosphorus | Contaminated Fish Tissue, Low DO | Category 5A | West Central Region |
| 1179900 | 530 | Wisconsin River (At Castle Rock Lake) | Adams, Juneau | 159 | 173.27 | Low Priority | Contam. Sediment, Other Factors , PS/NPS Blend | 303d Listed | Dioxin, Mercury, PCBs, Total Nitrogen | Contaminated Fish Tissue, Low DO, pH | Category 5A | West Central Region |
| 1179900 | 530 | Wisconsin River (At Petenwell Lake) | Adams, Juneau | 173 | 187.81 | Low Priority | Contam. Sediment, PS/NPS Blend | 303d Listed | Dioxin, Mercury, PCBs, Total Phosphorus | Contaminated Fish Tissue, Low DO | Category 5A | West Central Region |
| 1179900 | 530, 530, 535 included | Wisconsin River | Adams, Juneau, Wood | 188 | 204.17 | Low Priority | Contam. Sediment | 303d Listed, Deletion | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 175700 | 603 | Mason Lake* | Adams, Marquette | 0 | 846.99 | Low Priority | NPS | 303d Listed | Total Phosphorus | Excess Algal(Plant)Growth, pH | Category 5A | Northeast Region, West Central Region |
| 2403200 | 29 | Bear Lake | Ashland | 0 | 204 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2753770 | 72 | Chequamegon Bay (Ashland Coal Tar Site) | Ashland | 0 | 16.62 | Low Priority | Contam. Sediment | 303d Listed | PAHs | Chronic Aquatic Toxicity, Contaminated Sediment | Category 5A | Northern Region |
| 2430300 | 100 | Day Lake | Ashland | 0 | 625 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2914800 | 132 | English Lake | Ashland | 0 | 231.55 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 1850200 | 161 | Gates Lake | Ashland | 0 | 22 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2935500 | 160 | Lake Galilee | Ashland | 0 | 211.55 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2751220 | 829 | Lake Superior, Maslowski Beach | Ashland | 0 | 0.87 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | Northern Region |
| 2915800 | 486 | Lake Three | Ashland | 0 | 61.4 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2916900 | 292 | Mineral Lake | Ashland | 0 | 227.06 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2917200 | 371 | Potter Lake | Ashland | 0 | 29.16 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2918600 | 446 | Spider Lake | Ashland | 0 | 86.39 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2936200 | 448 | Spillerberg Lake | Ashland | 0 | 74.91 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2283300 | 65 | Butternut Lake | Ashland, Price | 0 | 1006 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2401300 | 49 | Black Lake | Ashland, Sawyer | 0 | 129 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 1832800 | 24 | Bass Lake | Barron | 0 | 118 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2081200 | 32 | Beaver Dam Lake | Barron | 0 | 1112 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2089000 | 100000 | Chetek River | Barron | 0 | 5 | Low Priority | PS/NPS Blend | Proposed for Listing | Total Phosphorus | Eutrophication, Low DO | Category 5A | Northern Region |
| 2630200 | 129 | Echo Lake | Barron | 0 | 161 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2094000 | 812 | Lake Chetek | Barron | 0 | 770 | Low Priority | NPS | 303d Listed | Total Phosphorus | Eutrophication | Category 5A | Northern Region |
| 2104500 | 106 | Lake Desair | Barron | 0 | 79.48 | Low Priority | NPS | 303d Listed | Sediment, Total Phosphorus | Degraded Habitat, Eutrophication | Category 5A | Northern Region |
| 2478600 | 254 | Loon Lake | Barron | 0 | 94 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2094600 | 830 | Mud (Ojaski) Lake | Barron | 0 | 577 | Low Priority | NPS | 303d Listed | Total Phosphorus | Eutrophication | Category 5A | Northern Region |
| 2630800 | 317 | North Lake | Barron | 0 | 89 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2094300 | 834 | Pokegama Lake | Barron | 0 | 506 | Low Priority | NPS | 303d Listed | Total Phosphorus | Eutrophication | Category 5A | Northern Region |
| 2094100 | 835 | Prairie Lake | Barron | 0 | 1534 | Low Priority | NPS | 303d Listed | Total Phosphorus | Eutrophication, Total Phosphorus | Category 5A | Northern Region |
| 2063500 | 604, 836 | Red Cedar River | Barron | 73.6 | 78.51 | Low Priority | Atm. Deposition, Other Factors , PS/NPS Blend | 303d Listed, Deletion | Mercury, PCBs, Total Phosphorus | Contaminated Fish Tissue, Low DO | Category 5A | Northern Region |
| 2063500 | 582, 836 | Red Cedar River | Barron | 78.5 | 100.7 | Low Priority | Atm. Deposition, Other Factors | 303d Listed | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | Northern Region |
| 2630700 | 419 | Scott Lake | Barron | 0 | 81 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 1884800 | 481 | Sylvan Lake | Barron | 0 | 67 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2089500 | 842 | Tenmile Lake | Barron | 0 | 376 | Low Priority | NPS | 303d Listed | Total Phosphorus | Eutrophication | Category 5A | Northern Region |
| 2063500 | 381 | Red Cedar River | Barron, Dunn | 28.7 | 73.6 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region, West Central Region |
| 2754200 | 8 | Anderson Lake | Bayfield | 0 | 31.05 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 2756200 | 53 | Bladder Lake | Bayfield | 0 | 84.06 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2903800 | 354 (in part) | Buskey Bay Lake (Pike Chain Of Lakes) | Bayfield | 0 | 88.28 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2899200 | 81 | Cisco Lake | Bayfield | 0 | 96.27 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2897100 | 108 | Diamond Lake | Bayfield | 0 | 322.37 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2902900 | 354 (in part) | Eagle Lake (Pike Chain Of Lakes) | Bayfield | 0 | 163.42 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2902800 | 354 (in part) | Flynn Lake (Pike Chain Of Lakes) | Bayfield | 0 | 29.59 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2903200 | 354 (in part) | Hart Lake (Pike Chain Of Lakes) | Bayfield | 0 | 256.87 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2902600 | 354 (in part) | Hildur Lake (Pike Chain Of Lakes) | Bayfield | 0 | 63.13 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2751220 | 100000 | Lake Superior, Thompson West End Park | Bayfield | 0 | 0.53 | Low Priority | Other Factors | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | Northern Region |
| 2473500 | 482 | Lake Tahkodah | Bayfield | 0 | 147.83 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2767100 | 252 | Long Lake T47 R8w S2 | Bayfield | 0 | 279.62 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | Northern Region |
| 2767200 | 253 | Long Lake T48 R5w S6 | Bayfield | 0 | 32.08 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2903700 | 354 (in part) | Millicent Lake (Pike Chain Of Lakes) | Bayfield | 0 | 182.69 | Low Priority | Contam. Sediment | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2770700 | 338 | Perch Lake T45 R7w S5 | Bayfield | 0 | 68.89 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2904000 | 354 (in part) | Pike Lake (Pike Chain Of Lakes) | Bayfield | 0 | 19.45 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2882300 | 437 | Siskiwit Lake | Bayfield | 0 | 284.8 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2903100 | 354 (in part) | Twin Bear Lake (Pike Chain Of Lakes) | Bayfield | 0 | 157.16 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2832200 | 512 | Twin Lake West | Bayfield | 0 | 15.07 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Atmospheric Deposition - Toxics | Category 5B | Northern Region |
| 124100 | 12 | Apple Creek | Brown | 0 | 3.99 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northeast Region |
| 122200 | 100000 | Ashwaubenon Creek | Brown | 0 | 15 | High Priority | PS/NPS Blend | Proposed for Listing | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 118100 | 802 | Baird Creek | Brown | 0 | 3.5 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northeast Region |
| 118100 | 100000 | Baird Creek | Brown | 3.5 | 13.1 | High Priority | PS/NPS Blend | Proposed for Listing | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 118400 | 100000 | Bower Creek | Brown | 0 | 3 | High Priority | NPS | Proposed for Listing | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | Northeast Region |
| 118400 | 100000 | Bower Creek | Brown | 3 | 13 | High Priority | NPS | Proposed for Listing | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | Northeast Region |
| 409700 | 116 | Duck Creek | Brown | 0 | 4.96 | High Priority, Low Priority | Atm. Deposition, NPS | 303d Listed, TMDL Development | Mercury, Sediment, Total Phosphorus | Contaminated Fish Tissue, Low DO, Sediment | Category 5A | Northeast Region |
| 121600 | 120 | Dutchman Creek | Brown | 0 | 4.04 | High Priority, Low Priority | NPS | 303d Listed, TMDL Development | Ammonia (Unionized) - Toxin, Total Phosphorus | Chronic Aquatic Toxicity, Low DO | Category 5A | Northeast Region |
| 118000 | 124 | East River | Brown | 0 | 14.15 | High Priority, Low Priority | NPS | 303d Listed, TMDL Development | Sediment, Total Phosphorus, Unspecified Metals | Chronic Aquatic Toxicity, Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 70 | 174 | Green Bay (Inner Bay, Aoc) | Brown | 0 | 13867.4 | High Priority | Contam. Sediment, NPS, PS/NPS Blend | 303d Listed, Addition, TMDL Development | PCBs, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 117900 | 149, 173, 149, 173 | Lower Fox River (Mouth To Depere Dam) | Brown | 0 | 7.39 | High Priority, Low Priority | Contam. Sediment, PS/NPS Blend | Addition, EAP Project, TMDL Development | PCBs, Sediment, Total Phosphorus | Contaminated Fish Tissue, Contaminated Sediment, Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 125100 | 368 | Plum Creek | Brown | 0 | 13.86 | High Priority | PS/NPS Blend | Addition, TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature | Category 5A | Northeast Region |
| 118000 | 125 | East River | Brown, Calumet | 14.2 | 42.25 | High Priority, Low Priority | NPS | 303d Listed, TMDL Development | Sediment, Total Phosphorus, Unspecified Metals | Chronic Aquatic Toxicity, Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 125100 | 368 | Plum Creek | Brown, Calumet | 13.9 | 16.42 | High Priority | PS/NPS Blend | TMDL Development | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | Northeast Region |
| 90700 | 219 | Kewaunee River | Brown, Kewaunee | 16.4 | 27.89 | Low Priority | Other Factors | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | Northeast Region |
| 71300 | 614 | Branch River | Brown, Manitowoc | 20.2 | 36.78 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | Northeast Region |
| 124100 | 11 | Apple Creek | Brown, Outagamie | 3.99 | 23.88 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northeast Region |
| 409700 | 116 | Duck Creek | Brown, Outagamie | 4.96 | 25.69 | NA | PS/NPS Blend | Deletion | Sediment, Total Phosphorus | Low DO, Sediment | Category 5A | Northeast Region |
| 121600 | 120 | Dutchman Creek | Brown, Outagamie | 4.04 | 17.97 | NA | NPS | Deletion | Ammonia (Unionized) - Toxin, Sediment | Chronic Aquatic Toxicity, Degraded Habitat | Category 5A | Northeast Region |
| 117900 | 150 | Lower Fox River (Depere Dam To Middle Appleton Dam) | Brown, Outagamie | 7.39 | 32.18 | High Priority, Low Priority | Contam. Sediment, PS/NPS Blend | EAP Project, TMDL Development | PCBs, Total Phosphorus | Contaminated Fish Tissue, Low DO | Category 5A | Northeast Region |
| 410200 | 490 | Trout Creek | Brown, Outagamie | 0 | 12.77 | NA | NPS | Deletion | Sediment, Total Phosphorus | Low DO, Sediment | Category 5A | Northeast Region |
| 1813100 | 60 | Buell Valley Creek | Buffalo | 0 | 2.32 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1813600 | 88 | Cochrane Ditch (Rose Valley Cr) | Buffalo | 0 | 10.06 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1808400 | 121 | Eagle Creek | Buffalo | 9.09 | 17.56 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1811400 | 196 | Irish Valley Creek | Buffalo | 0 | 7.89 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1810800 | 204 | Jahns Valley Creek | Buffalo | 0 | 7.71 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1808900 | 209 | Joos Valley Creek | Buffalo | 0 | 7.44 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 2048000 | 238 | Little Bear Creek | Buffalo | 0 | 4.35 | Delisted 2002 | PS/NPS Blend | Water Delisted | Sediment | Degraded Habitat | Category 2 | West Central Region |
| 1776000 | 479 | Swinns Valley Creek | Buffalo | 0 | 8.49 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | West Central Region |
| 1813000 | 701 | Weiland Valley Creek | Buffalo | 0.01 | 3.22 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5C | West Central Region |
| 1811200 | 541 | Wolf Valley Creek | Buffalo | 0 | 2.7 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | West Central Region |
| 1810200 | 547 | Yeager Valley Creek | Buffalo | 0 | 4.43 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | West Central Region |
| 2050000 | 80 | Chippewa River | Buffalo, Pepin | 0 | 20.73 | Low Priority | Atm. Deposition, Contam. Sediment | Addition, Deletion | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 1769900 | 489 | Trempealeau River | Buffalo, Trempealeau | 0 | 34.28 | Low Priority | Other Factors | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2651800 | 118 | Dunham Lake | Burnett | 0 | 243 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2471600 | 208 | Johnson Lake | Burnett | 0 | 397 | Low Priority | Contam. Sediment | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2649500 | 303 | Mud Hen Lake | Burnett | 0 | 563 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2640100 | 410 | Round Lake T37n R18w S27 | Burnett | 0 | 204 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2495100 | 319 | Sand Lake T40n R15w S25 | Burnett | 0 | 962 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2675200 | 548 | Yellow Lake | Burnett | 0 | 2287 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 80200 | 210 | Jordan Creek | Calumet | 0 | 1.36 | Low Priority | Contam. Sediment | EAP Project | PCBs | Contaminated Sediment | Category 5A | Northeast Region |
| 78200 | 221 | Killsnake River | Calumet | 0 | 19.73 | Delisted 2002 | Contam. Sediment | Water Delisted | PCBs | PCBs | Category 2 | Northeast Region |
| 75900 | 265 | North Branch Manitowoc River | Calumet | 0 | 7.35 | Low Priority | PS/NPS Blend | 303d Listed | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 79900 | 359 | Pine Creek | Calumet | 0 | 5.54 | Low Priority | Contam. Sediment | EAP Project | PCBs | Contaminated Sediment | Category 5A | Northeast Region |
| 79900 | 358 | Pine Creek | Calumet | 5.54 | 9.12 | Low Priority | Contam. Sediment | EAP Project | PCBs | Contaminated Sediment | Category 5A | Northeast Region |
| 125100 | 368 | Plum Creek | Calumet | 16.4 | 19.5 | High Priority | PS/NPS Blend | TMDL Development | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | Northeast Region |
| 3000057 | 649 | Unnamed | Calumet | 0 | 2.92 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 131100 | 523 | Lake Winnebago | Calumet, Fond du Lac, Winnebago | 0 | 131871 | Low Priority, Medium Priority | Atm. Deposition, Contam. Sediment, NPS | 303d Listed, Deletion | Mercury, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Eutrophication, Low DO | Category 5A | Northeast Region |
| 71000 | 262 | Manitowoc River | Calumet, Manitowoc | 20.7 | 35.81 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Sediment | Category 5A | Northeast Region |
| 77900 | 264 | South Branch Manitowoc River | Calumet, Manitowoc | 0 | 12.64 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Sediment | Category 5A | Northeast Region |
| 126800 | 215 | Kankapot Creek | Calumet, Outagamie | 2.66 | 9.57 | High Priority | NPS, PS/NPS Blend | Addition, TMDL Development | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | Northeast Region |
| 2050000 | 538, 80 | Chippewa R At L Wissota | Chippewa | 77 | 80.18 | Low Priority | Atm. Deposition, Contam. Sediment, PS/NPS Blend | 303d Listed, Addition, Deletion | Mercury, PCBs, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 2050000 | 80 | Chippewa River | Chippewa | 80.2 | 105.75 | Low Priority | Atm. Deposition, Contam. Sediment | Addition, Deletion | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2050000 | 675, 76 | Chippewa River (At Holcombe Flowage) | Chippewa | 106 | 110.14 | Delisted 2006 | Atm. Deposition, Contam. Sediment | Delist, Water Delisted | Mercury, PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 2 | West Central Region |
| 2175700 | 135, 135 | Finley Lake | Chippewa | 0 | 57.99 | Low Priority | NPS | 303d Listed | Sediment, Total Phosphorus | Degraded Habitat, Eutrophication, pH | Category 5A | West Central Region |
| 2150200 | 179 | Hallie Lake | Chippewa | 0 | 78.64 | Medium Priority | NPS | 303d Listed | Mercury, Sediment | Contaminated Fish Tissue, Degraded Habitat, Eutrophication, pH | Category 5A | West Central Region |
| 1853400 | 183 | Hemlock Lake | Chippewa | 0 | 28 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 2184900 | 675, 76 | Holcombe Flowage South | Chippewa | 0 | 1338.83 | Low Priority | Atm. Deposition, Contam. Sediment | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 1854300 | 191 | Horseshoe Lake | Chippewa | 0 | 24 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1855100 | 192 | Howe Lake | Chippewa | 0 | 68 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 2151400 | 239 | Little Hay Creek | Chippewa | 0 | 2.14 | NA | NPS | Delist | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature, Low DO | Category 2 | West Central Region |
| 1869300 | 306 | North Shattuck Lake | Chippewa | 0 | 39 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 2157000 | 601 | Otter Lake (Brown) | Chippewa | 0 | 601.56 | Medium Priority | NPS | 303d Listed | Total Phosphorus | Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 2173900 | 369 | Popple Lake | Chippewa | 0 | 94.3 | Low Priority | NPS | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 1876900 | 386 | Riley Lake | Chippewa | 0 | 27.23 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 2169200 | 409 | Round Lake T32 R9w S14 | Chippewa | 0 | 215.79 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1880000 | 705 | Sand Lake | Chippewa | 0 | 14.84 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1887500 | 496 | Two Island Lake | Chippewa | 0 | 29 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 2152800 | 538, 80 | Wissota Lake | Chippewa | 0 | 6300 | High Priority, Low Priority | Atm. Deposition, PS/NPS Blend | 303d Listed, TMDL Development | Mercury, PCBs, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Eutrophication, pH | Category 5A | West Central Region |
| 2146000 | 539 | Wolf River | Chippewa | 13.5 | 17.09 | Low Priority | Habitat/Physical, PS/NPS Blend | 303d Listed | Sediment, Total Phosphorus | Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 2050000 | 80 | Chippewa River | Chippewa, Eau Claire | 60.1 | 77.04 | Low Priority | Atm. Deposition, Contam. Sediment | Addition, Deletion | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2050000 | 675 | Chippewa River | Chippewa, Rusk | 110 | 144.18 | NA | Contam. Sediment | Delist | PCBs | Contaminated Fish Tissue | Category 2 | Northern Region, West Central Region |
| 2184900 | 77 | Holcombe Flowage North | Chippewa, Rusk | 0 | 1541.92 | Low Priority | Atm. Deposition, NPS | 303d Listed, Deletion | Mercury, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Eutrophication, pH | Category 5A | Northern Region, West Central Region |
| 2092900 | 360 | Pine Lake | Chippewa, Rusk | 0 | 262 | Low Priority | Contam. Sediment | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region, West Central Region |
| 1676700 | 51 | Black River | Clark | 77.2 | 90.64 | Low Priority | Other Factors | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 1676700 | 50 | Black River, Hwy H To Rock Creek | Clark | 98.1 | 107.12 | Low Priority | Other Factors , PS/NPS Blend | 303d Listed | Mercury, Unknown Pollutant | Contaminated Fish Tissue, Low DO | Category 5A | West Central Region |
| 2143900 | 277 | Mead Lake | Clark | 0 | 310.27 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Excess Algal(Plant)Growth, Total Phosphorus, pH | Category 5A | West Central Region |
| 2139000 | 391 | Rock Dam Lake | Clark | 0 | 125 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1736200 | 428 | Sherwood Lake* | Clark | 0 | 117 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1727700 | 626 | Arbutus Lake* | Clark, Jackson | 0 | 839 | Low Priority | Other Factors | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | West Central Region |
| 1676700 | 582 | Black R. (Below Medford) | Clark, Taylor | 133 | 168.4 | Low Priority | Other Factors | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | Northern Region, West Central Region |
| 180300 | 832 | Park Lake | Columbia | 0 | 312 | Medium Priority | NPS | 303d Listed | Sediment, Total Phosphorus | Eutrophication | Category 5A | South Central Region |
| 1263700 | 411 | Rowan Creek | Columbia | 0 | 10.41 | Delisted 2002 | PS/NPS Blend | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 117900 | 616 | Upper Fox River | Columbia | 161 | 165.16 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 1179900 | 622 | Wisconsin River | Columbia, Dane, Iowa, Sauk | 57.7 | 90.94 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 842500 | 90 | Crawfish River - Columbus Mill Pond | Columbia, Dodge | 0 | 18.38 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 117900 | 152 | Upper Fox River | Columbia, Marquette | 144 | 160.71 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | Northeast Region, South Central Region |
| 1260600 | 530 | Lake Wisconsin | Columbia, Sauk | 0 | 9000 | Low Priority | Contam. Sediment, Other Factors | 303d Listed | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 1179900 | 530 | Wisconsin River | Columbia, Sauk | 90.9 | 116.16 | Low Priority | Contam. Sediment, Other Factors | 303d Listed | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 1179900 | 530 | Wisconsin River | Columbia, Sauk | 116 | 138.07 | Low Priority | Contam. Sediment, Other Factors | 303d Listed | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | South Central Region |
| 1184300 | 180 | Halls Br | Crawford | 1.97 | 5.16 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | West Central Region |
| 1182400 | 220 | Kickapoo River | Crawford | 19.1 | 25.45 | Low Priority | Other Factors | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 1184800 | 415 | Sand Creek | Crawford | 0 | 5.99 | Delisted 2002 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | West Central Region |
| 1179900 | 622 | Wisconsin River | Crawford, Grant | 0 | 27.67 | Low Priority | Contam. Sediment | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | South Central Region, West Central Region |
| 1179900 | 622 | Wisconsin River | Crawford, Grant, Iowa, Richland | 27.7 | 57.66 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | South Central Region, West Central Region |
| 799500 | 16 | Badfish Creek | Dane | 12.3 | 13.18 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 5A | South Central Region |
| 888100 | 17 | Badger Mill Creek | Dane | 2 | 5 | Delisted 2002 | Other Factors | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 909200 | 162 | German Valley Br | Dane | 0 | 7.63 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 1248800 | 178 | Halfway Prairie Creek | Dane | 0 | 8 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 887800 | 185 | Henry Creek | Dane | 0 | 0.98 | Delisted 2006 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 805400 | 280 | Lake Mendota | Dane | 0 | 9780.89 | Low Priority | Other Factors | 303d Listed | PCB-1242 | Contaminated Fish Tissue | Category 5A | South Central Region |
| 805400 | 100000 | Lake Mendota, , Spring Harbor Beach | Dane | 0 | 0.1 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 805400 | 100000 | Lake Mendota, James Madison Park Beach | Dane | 0 | 0.36 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 805400 | 100000 | Lake Mendota, Marshall Park Beach | Dane | 0 | 0.22 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 804600 | 299 | Lake Monona | Dane | 0 | 3357.56 | Low Priority | Atm. Deposition, Contam. Sediment | 303d Listed, Deletion | Mercury, PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 5A | South Central Region |
| 804600 | 100000 | Lake Monona, Bernies Beach | Dane | 0 | 0.09 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 804600 | 100000 | Lake Monona, Brittingham Beach | Dane | 0 | 0.34 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 804600 | 100000 | Lake Monona, Esther Park Beach | Dane | 0 | 0.15 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 804600 | 100000 | Lake Monona, Olbrich Park Beach | Dane | 0 | 0.23 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 804600 | 100000 | Lake Monona, Olin Park Beach | Dane | 0 | 0.07 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 803700 | 506 | Lake Waubesa | Dane | 0 | 2074.53 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | South Central Region |
| 805000 | 100000 | Lake Wingra, Vilas Park Beach | Dane | 0 | 0.25 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | South Central Region |
| 837500 | 553 | Maunesha River | Dane | 13.2 | 31.8 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 804700 | 522 | Murphy (Wingra) Creek | Dane | 0 | 1.2 | Low Priority | Contam. Sediment | 303d Listed | Unknown Pollutant | Chronic Aquatic Toxicity | Category 5A | South Central Region |
| 804200 | 704 | Nine Springs Creek | Dane | 0 | 6.16 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Elevated Water Temperature, Low DO | Category 5A | South Central Region |
| 805900 | 641 | Pheasant Br | Dane | 0 | 1 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 805900 | 641 | Pheasant Br | Dane | 1 | 9.09 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 908500 | 367 | Pleasant Valley Br | Dane | 0 | 5.92 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 805600 | 660 | Spring (Dorn) Creek | Dane | 1 | 6.46 | High Priority, Low Priority | NPS | 303d Listed, TMDL Development | Escherichia coli, Sediment | Degraded Habitat, Elevated Water Temperature, Escherichia coli | Category 5A | South Central Region |
| 805100 | 467 | Starkweather Creek | Dane | 0 | 3.65 | Low Priority | Contam. Sediment, NPS | 303d Listed | BOD, Sediment, Unspecified Metals | Chronic Aquatic Toxicity, Degraded Habitat, Low DO | Category 5A | South Central Region |
| 908200 | 480 | Syftestad Creek | Dane | 0 | 5.16 | Delisted 2006 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 806600 | 487 | Token Creek | Dane | 2.9 | 6.35 | Implementation Priority | Habitat/Physical, NPS | TMDL Approved | Sediment | Sediment | Category 5C | South Central Region |
| 806600 | 488 | Token Creek | Dane | 6.35 | 9.6 | Implementation Priority | Habitat/Physical, NPS | TMDL Approved | Fish Barriers (Fish Passage), Sediment | Fish Barriers (Fish Passage), Sediment | Category 5C | South Central Region |
| 1249200 | 710 | Vermont Creek | Dane | 0 | 3.46 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | South Central Region |
| 1248900 | 511 | Wendt Creek | Dane | 0 | 3.63 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 1248900 | 510 | Wendt Creek | Dane | 3.63 | 8.27 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 886100 | 846 | West Branch Sugar River | Dane | 0 | 7.64 | Delisted 2004 | PS/NPS Blend | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 886100 | 847 | West Branch Sugar River | Dane | 7.65 | 18.82 | Delisted 2004 | PS/NPS Blend | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | South Central Region |
| 798300 | 546 | Yahara, Stoughton To L. Kegonsa | Dane | 16.3 | 22.06 | High Priority, Medium Priority | PS/NPS Blend | 303d Listed, TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO, Turbidity | Category 5A | South Central Region |
| 840800 | 302 | Mud Creek | Dane, Dodge | 0 | 10.77 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 837600 | 840 | Stony Brook | Dane, Dodge, Jefferson | 0 | 15 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 837500 | 272 | Maunesha River | Dane, Jefferson | 5.49 | 13.21 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 808700 | 610 | Lake Koshkonong | Dane, Jefferson, Rock | 0 | 10595.6 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Excess Algal(Plant)Growth, Low DO, Sediment | Category 5A | South Central Region |
| 799500 | 16 | Badfish Creek | Dane, Rock | 0 | 12.3 | Low Priority | Contam. Sediment | 303d Listed | PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 5A | South Central Region |
| 798300 | 545 | Yahara R. Badfish Cr To Stoughton | Dane, Rock | 7.29 | 16.32 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO, Turbidity | Category 5A | South Central Region |
| 835900 | 6 | Alto Creek | Dodge | 0 | 6.15 | High Priority | PS/NPS Blend | TMDL Development | Sediment | Degraded Habitat, Low flow alterations | Category 5A | South Central Region |
| 856000 | 803 | Baker Creek | Dodge | 0 | 10 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 831400 | 33 | Beaver Dam River | Dodge | 0 | 11.06 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 831400 | 34 | Beaver Dam River | Dodge | 11.1 | 14.15 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 831400 | 35 | Beaver Dam River | Dodge | 14.2 | 30.14 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 834900 | 808 | Calamus Creek | Dodge | 0 | 17 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 832100 | 68 | Casper Creek | Dodge | 0 | 2.36 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 855400 | 99 | Davy Creek | Dodge | 0 | 5.69 | Low Priority | Contam. Sediment | 303d Listed | Unspecified Metals | Chronic Aquatic Toxicity | Category 5A | South Central Region |
| 860000 | 816 | Dead Creek | Dodge | 0 | 3.92 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 860000 | 816 | Dead Creek | Dodge | 3.92 | 10.52 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 861400 | 818 | East Branch Rock River | Dodge | 0 | 11.61 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 835800 | 820 | Fox Lake | Dodge | 0 | 2625 | High Priority | Habitat/Physical, NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Eutrophication, Fish Kills | Category 5A | South Central Region |
| 861700 | 167 | Gill Creek | Dodge | 0 | 6.32 | High Priority, Medium Priority | NPS | 303d Listed, TMDL Development | Ammonia (Unionized) - Toxin, Sediment, Total Phosphorus | Acute Aquatic Toxicity, Degraded Habitat | Category 5A | South Central Region |
| 861200 | 190 | Horicon Marsh | Dodge | 0 | 1000 | High Priority | NPS, PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 861600 | 195, 195 | Irish Creek | Dodge | 0 | 3.79 | High Priority, Medium Priority | NPS | 303d Listed, TMDL Development | Ammonia (Unionized) - Toxin, Sediment, Total Phosphorus | Acute Aquatic Toxicity, Degraded Habitat | Category 5A | South Central Region |
| 863500 | 225, 225 | Kiefer Creek, Kummel Creel | Dodge | 0 | 10.38 | High Priority, Medium Priority | PS/NPS Blend | 303d Listed, TMDL Development | Ammonia (Unionized) - Toxin, Sediment, Total Phosphorus | Acute Aquatic Toxicity, Degraded Habitat, Low DO | Category 5A | South Central Region |
| 863500 | 225 | Kiefer Creek, Kummel Creel | Dodge | 10.4 | 11.54 | High Priority | NPS, PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 831600 | 826 | Lau Creek | Dodge | 0 | 6 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 834400 | 335 | Park Creek | Dodge | 0 | 2.37 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 788800 | 395 | Rock River | Dodge | 296 | 304.88 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | South Central Region |
| 833800 | 418 | Schultz Creek | Dodge | 0 | 4.71 | High Priority | NPS | TMDL Development | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 20 | 838 | Sinissippi Lake - Neider Park Landing | Dodge | 0 | 0.4 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | South Central Region |
| 859900 | 402 | Sinissippi Lake (Hustisford) | Dodge | 0 | 1647.77 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Eutrophication | Category 5A | South Central Region |
| 863500 | 226 | Kiefer Creek, Kummel Creel | Dodge, Fond du Lac | 11.5 | 14 | High Priority | NPS, PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region, South Central Region |
| 861300 | 845 | West Branch Rock River | Dodge, Fond du Lac | 50 | 87.63 | High Priority | NPS | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | Northeast Region, South Central Region |
| 837500 | 271 | Maunesha River | Dodge, Jefferson | 0 | 5.5 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 788800 | 609 | Rock River | Dodge, Jefferson | 214 | 249.13 | High Priority | PS/NPS Blend | TMDL Development | Total Phosphorus | Excess Algal(Plant)Growth, Low DO | Category 5A | South Central Region |
| 788800 | 396 | Rock River | Dodge, Jefferson | 270 | 293.25 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat | Category 5A | South Central Region |
| 94800 | 3 | Ahnapee River | Door | 7.86 | 14.71 | Low Priority | Other Factors | 303d Listed | PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 5A | Northeast Region |
| 97700 | 84 | Clark Lake | Door | 0 | 865.13 | NA | Contam. Sediment | Delist | PCBs | Contaminated Sediment | Category 2 | Northeast Region |
| 93500 | 260 | Mackaysee Lake | Door | 0 | 347 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northeast Region |
| 88 | 471 | Sturgeon Bay | Door | 0 | 4944.63 | Delisted 2002 | Contam. Sediment | Water Delisted | Unknown Pollutant | Chronic Aquatic Toxicity | Category 2 | Northeast Region |
| 20 | 841 | Sunset Beach - Sturgeon Bay (L. Michigan) | Door | 0 | 0.55 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | Northeast Region |
| 94800 | 3 | Ahnapee River | Door, Kewaunee | 0 | 7.86 | Low Priority | Other Factors | 303d Listed | PCBs | Contaminated Fish Tissue, Contaminated Sediment | Category 5A | Northeast Region |
| 96100 | 470 | Stony Creek | Door, Kewaunee | 0 | 8.26 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 2751400 | 5 | Allouez Bay, St Louis River Aoc | Douglas | 0 | 1 | Low Priority | Contam. Sediment | Addition, Deletion | Mercury, PCBs | Contaminated Fish Tissue | Category 5A | Northern Region |
| 2858100 | 7, 7 | Amnicon Lake | Douglas | 0 | 390.23 | Low Priority | Atm. Deposition, NPS | 303d Listed | Mercury, Sediment, Total Phosphorus | Contaminated Fish Tissue, Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northern Region |
| 2835500 | 91 | Crawford Creek | Douglas | 0 | 9.12 | Low Priority | Contam. Sediment | 303d Listed | Creosote, PAHs | Chronic Aquatic Toxicity | Category 5A | Northern Region |
| 2838000 | 723 | Interfalls Lake, Pattison Beach (State Park) | Douglas | 0 | 0.07 | Delisted 2006, Low Priority | NPS, Other Factors | Proposed for Listing, Water Delisted | Escherichia coli | Elevated Bacteria | Category 5A | Northern Region |
| 2866200 | 628 | Lake Minnesuing | Douglas | 0 | 450.24 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2751220 | 100000 | Lake Superior, Amnicon River Beach | Douglas | 0 | 0.25 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | Northern Region |
| 2751220 | 804 | Lake Superior, Barker's Island Inner | Douglas | 0 | 0.4 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | Northern Region |
| 2751220 | 806 | Lake Superior, Brule River State Forest #2 | Douglas | 0 | 0.36 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | Northern Region |
| 2751220 | 807 | Lake Superior, Brule River State Forest #3 | Douglas | 0 | 0.69 | Low Priority | Other Factors | 303d Listed | Escherichia coli | Escherichia coli | Category 5A | Northern Region |
| 2751220 | 100000 | Lake Superior, Middle River Beach | Douglas | 0 | 0.5 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | Northern Region |
| 2751220 | 100000 | Lake Superior, Wisconsin Point Beach #2 | Douglas | 0 | 0.48 | Low Priority | Other Factors | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | Northern Region |
| 2856400 | 627 | Lyman Lake | Douglas | 0 | 370.45 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2843650 | 312 | Newton Creek | Douglas | 0 | 1.76 | Medium Priority | Contam. Sediment | 303d Listed | Foam/Flocs/Scum/Oil Slicks, PAHs, Unspecified Metals | Chronic Aquatic Toxicity | Category 5A | Northern Region |
| 2492100 | 382 | Red Lake | Douglas | 0 | 258 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2740300 | 464 | St Croix Flowage | Douglas | 0 | 1913 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 2751300 | 187 | Superior Bay, Hog Island Inlet | Douglas | 0 | 18.26 | Medium Priority | Contam. Sediment | 303d Listed | Foam/Flocs/Scum/Oil Slicks, PAHs, Unspecified Metals | Chronic Aquatic Toxicity | Category 5A | Northern Region |
| -348562 | 92 | Trib To Crawford Creek | Douglas | 0 | 0.51 | Low Priority | Contam. Sediment | 303d Listed | Creosote, PAHs | Chronic Aquatic Toxicity | Category 5A | Northern Region |
| 2692900 | 294 | Minong Flowage*(L Nancy) | Douglas, Washburn | 0 | 1564 | NA | Atm. Deposition | Delist | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 2066300 | 82 | Clack Creek | Dunn | 0 | 3.34 | Delisted 2002 | Habitat/Physical | Water Delisted | Elevated Water Temperature, Sediment | Degraded Habitat, Elevated Water Temperature | Category 2 | West Central Region |
| 2066400 | 642 | Coon Creek | Dunn | 0 | 3.35 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | West Central Region |
| 2064600 | 165 | Gilbert Creek | Dunn | 0 | 10.45 | Delisted 2002 | Habitat/Physical | Water Delisted | Elevated Water Temperature, Sediment | Degraded Habitat, Elevated Water Temperature | Category 2 | West Central Region |
| 2056800 | 223 | Knights Creek | Dunn | 0 | 8 | Delisted 2002 | PS/NPS Blend | Water Delisted | Sediment | Degraded Habitat | Category 2 | West Central Region |
| 2065900 | 281 | Lake Menomin | Dunn | 0 | 1008.65 | High Priority | PS/NPS Blend | TMDL Development | Total Phosphorus | Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 1871400 | 328 | Old Elk Lake | Dunn | 0 | 90.16 | Low Priority | NPS | 303d Listed | Sediment, Total Phosphorus | Degraded Habitat, Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 2063500 | 836 | Red Cedar River | Dunn | 0 | 9.27 | Low Priority | Other Factors | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2063500 | 380, 836 | Red Cedar River | Dunn | 9.27 | 13.56 | Low Priority | NPS, Other Factors | 303d Listed | PCBs, Total Phosphorus | Contaminated Fish Tissue, Excess Algal(Plant)Growth, pH | Category 5A | West Central Region |
| 2063500 | 836 | Red Cedar River | Dunn | 13.6 | 16.48 | Low Priority | Other Factors | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2063500 | 281 | Red Cedar River | Dunn | 16.5 | 18.8 | Low Priority | NPS | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2063500 | 483 | Red Cedar River | Dunn | 22.5 | 28.72 | High Priority, Low Priority | Atm. Deposition, PS/NPS Blend | 303d Listed, TMDL Development | Degraded Habitat, Total Phosphorus | Degraded Habitat, Excess Algal(Plant)Growth, Total Phosphorus, pH | Category 5A | West Central Region |
| 2119000 | 659 | Rock Creek | Dunn | 2.8 | 4.64 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | West Central Region |
| 2068000 | 483 | Tainter Lake | Dunn | 0 | 1387.21 | High Priority | Atm. Deposition, PS/NPS Blend | Deletion, TMDL Development | Mercury, Total Phosphorus | Contaminated Fish Tissue, Eutrophication, pH | Category 5A | West Central Region |
| 2050000 | 80 | Chippewa River | Dunn, Eau Claire | 37.6 | 58.84 | Low Priority | Contam. Sediment | Addition | PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2050000 | 80 | Chippewa River | Dunn, Pepin | 20.7 | 37.58 | Low Priority | Contam. Sediment | Addition | PCBs | Contaminated Fish Tissue | Category 5A | West Central Region |
| 2055700 | 297 | Missouri Creek | Dunn, Pierce | 8.59 | 13.83 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | West Central Region |
| 2050000 | 79, 80 | Chippewa R At Eau Claire | Eau Claire | 58.8 | 60.05 | Low Priority | Contam. Sediment | 303d Listed, Addition | PCBs, Unspecified Metals | Chronic Aquatic Toxicity, Contaminated Fish Tissue, Contaminated Sediment | Category 5A | West Central Region |
| 2125400 | 176 | Halfmoon Lake | Eau Claire | 0 | 135.14 | Implementation Priority | NPS | TMDL Approved | Total Phosphorus | Eutrophication, pH | Category 5C | West Central Region |
| 704400 | 629 | Brule River Flow (Wi-71 Acres) | Florence | 0 | 209.57 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 651600 | 130 | Emily Lake | Florence | 0 | 183.29 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 591600 | 416 | Sand Lake | Florence | 0 | 50 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 672300 | 420 | Sea Lion Lake | Florence | 0 | 122 | NA | Atm. Deposition | Delist | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 608400 | 504 | Van Zile Lake | Florence, Forest | 0 | 78 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 133300 | 662 | Anderson Creek | Fond du Lac | 0 | 7.26 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 137400 | 809 | Campground Creek | Fond du Lac | 0 | 1.66 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 137400 | 810 | Campground Creek | Fond du Lac | 1.67 | 7.26 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northeast Region |
| 138700 | 661 | De Neveu Creek | Fond du Lac | 11 | 11.88 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 136200 | 100000 | East Trib. To Parsons Cr | Fond du Lac | 0.01 | 1.89 | Implementation Priority | NPS | Proposed for Listing | Elevated Water Temperature, Sediment | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 133700 | 143 | Fond Du Lac River | Fond du Lac | 0 | 1.56 | Medium Priority | Contam. Sediment | 303d Listed | PCBs, Unspecified Metals | Chronic Aquatic Toxicity, Contaminated Fish Tissue | Category 5A | Northeast Region |
| 8900 | 145 | Forest Lake | Fond du Lac | 0 | 51 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northeast Region |
| 863500 | 226 | Kiefer Creek, Kummel Creel | Fond du Lac | 14 | 17.96 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 38700 | 100000 | Long Lake Kettle Moraine St. Park North Beach | Fond du Lac | 0 | 0.33 | Low Priority | NPS | Proposed for Listing | Escherichia coli | Elevated Bacteria | Category 5A | Northeast Region |
| 38200 | 273 | Mauthe Lake | Fond du Lac | 0 | 78 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northeast Region |
| 133500 | 663 | Mosher Creek | Fond du Lac | 0 | 3 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 136000 | 611 | Parsons Creek | Fond du Lac | 0 | 2.58 | Implementation Priority | PS/NPS Blend | TMDL Approved | Sediment, Total Phosphorus | Degraded Habitat | Category 5C | Northeast Region |
| 136800 | 664 | Sevenmile Creek | Fond du Lac | 0 | 11 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 146800 | 431 | Silver Creek | Fond du Lac | 11.4 | 13.38 | Low Priority, Medium Priority | Contam. Sediment, PS/NPS Blend | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | Northeast Region |
| 869800 | 398 | South Branch Rock River | Fond du Lac | 0 | 3.58 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 146800 | 431 | Silver Creek | Fond du Lac, Green Lake | 7.86 | 19.4 | Low Priority, Medium Priority | Contam. Sediment, PS/NPS Blend | 303d Listed | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5A | Northeast Region |
| 869800 | 394 | South Branch Rock River | Fond du Lac, Green Lake | 3.58 | 19.68 | High Priority | PS/NPS Blend | TMDL Development | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | Northeast Region |
| 38700 | 246 | Long Lake | Fond du Lac, Sheboygan | 0 | 427 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northeast Region, Southeast Region |
| 15000 | 619 | Milwaukee River | Fond du Lac, Washington | 68.5 | 103.34 | Delisted 2006 | Contam. Sediment | Water Delisted | PCBs | Contaminated Sediment | Category 2 | Northeast Region, Southeast Region |
| 132600 | 665 | Van Dyne Creek | Fond du Lac, Winnebago | 1 | 9.11 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 181400 | 13 | Arbutus Lake | Forest | 0 | 161 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 184500 | 102 | Deep Hole Lake | Forest | 0 | 97 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 406900 | 362 | Pine Lake | Forest | 0 | 1670 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 378400 | 389 | Roberts Lake | Forest | 0 | 452 | NA | Contam. Sediment | Delist | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 389700 | 242 | Little Sand Lake | Forest, Langlade | 0 | 243 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 1614300 | 214 | Julia Lake | Forest, Oneida | 0 | 401 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 1605800 | 423 | Sevenmile Lake | Forest, Oneida | 0 | 503 | Delisted 2006 | Atm. Deposition | Water Delisted | Mercury | Contaminated Fish Tissue | Category 2 | Northern Region |
| 716800 | 216 | Kentuck Lake | Forest, Vilas | 0 | 957 | Low Priority | Atm. Deposition | 303d Listed | Mercury | Contaminated Fish Tissue | Category 5B | Northern Region |
| 953200 | 801 | Bacon Branch | Grant | 0 | 5.96 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 1211300 | 134 | Castle Rock Creek | Grant | 17.1 | 21.38 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 965800 | 71 | Chase Creek | Grant | 0 | 1.15 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 950900 | 97 | Culver Br | Grant | 0 | 2.34 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 950900 | 96 | Culver Br | Grant | 2.3 | 4.24 | Delisted 2002 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 1211300 | 134 | Fennimore Fork (Castle Rock) | Grant | 21.4 | 26.25 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 1212600 | 607 | Gunderson Valley Creek | Grant | 0.01 | 5.4 | Implementation Priority | NPS | TMDL Approved | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5C | South Central Region |
| 953900 | 231 | Leggett Creek | Grant | 9 | 16.62 | Delisted 2002 | PS/NPS Blend | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 943000 | 257 | Louisburg Creek | Grant | 0 | 5.26 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 963400 | 268 | Martin Br | Grant | 0 | 4 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 963400 | 268 | Martin Br | Grant | 4 | 5.32 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 963400 | 268 | Martin Br | Grant | 5.32 | 9.94 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 955100 | 269 | Martinville Creek | Grant | 0 | 2.6 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 955100 | 269 | Martinville Creek | Grant | 2.59 | 5.05 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 951100 | 276 | Mcpherson Br | Grant | 1.5 | 3.83 | Delisted 2002 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 964300 | 403 | Rogers Br | Grant | 0 | 8 | Implementation Priority | NPS | TMDL Approved | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5C | South Central Region |
| 964300 | 404 | Rogers Br | Grant | 8 | 11.83 | Implementation Priority | NPS | TMDL Approved | Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5C | South Central Region |
| 966100 | 417 | Sandy Creek | Grant | 0.37 | 6.01 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 944600 | 441 | Snowden Br (Big Patch Creek) | Grant | 0 | 5 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 945800 | 514 | Whig Br | Grant | 9 | 13.11 | Delisted 2002 | NPS | Water Delisted | Sediment | Degraded Habitat | Category 2 | South Central Region |
| 896800 | 14 | Argus School Branch | Green | 0 | 2.37 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5C | South Central Region |
| 894700 | 724 | Beckman Lake | Green | 0 | 64.55 | Delisted 2006 | Other Factors | Water Delisted | Escherichia coli | Escherichia coli | Category 2 | South Central Region |
| 897300 | 59 | Buckskin School Creek | Green | 0 | 6.71 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 880500 | 708 | Burgy Creek | Green | 0 | 10.99 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat, Elevated Water Temperature | Category 5C | South Central Region |
| 901000 | 115 | Dougherty Creek | Green | 14 | 16.59 | High Priority, Implementation Priority | NPS | TMDL Approved, TMDL Development | BOD, Sediment, Total Phosphorus | Degraded Habitat, Low DO | Category 5A | South Central Region |
| 892300 | 189 | Honey Creek | Green | 0.62 | 9.88 | High Priority | PS/NPS Blend | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 892300 | 188 | Honey Creek | Green | 9.88 | 16.48 | High Priority | PS/NPS Blend | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 882900 | 232 | Legler School Br | Green | 0.01 | 5.5 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 877700 | 211 | North Fork Juda Br | Green | 0 | 3.8 | Low Priority | PS/NPS Blend | 303d Listed | BOD, Total Phosphorus | Low DO | Category 5A | South Central Region |
| 883100 | 365 | Pioneer Valley Creek | Green | 0 | 4.16 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 901500 | 709 | Prairie Brook | Green | 0 | 3.11 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 879500 | 421 | Searles Creek | Green | 0 | 10.33 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 880400 | 435 | Silver School Br | Green | 0 | 6.14 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 877000 | 457 | Spring Creek | Green | 0 | 10.31 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 891300 | 493 | Twin Grove Br | Green | 0 | 5.96 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 146100 | 623 | Green Lake (Big Green) | Green Lake | 0 | 7485.65 | Low Priority | Atm. Deposition | 303d Listed | PCBs | Contaminated Fish Tissue | Category 5A | Northeast Region |
| 143700 | 666 | Harrington Creek | Green Lake | 0 | 2.97 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 146200 | 667 | Hill Creek | Green Lake | 0 | 1.84 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 162500 | 828 | Little Green Lake | Green Lake | 0 | 466 | Low Priority | NPS | 303d Listed | Total Phosphorus | Degraded Habitat, Eutrophication, Low DO, pH | Category 5A | Northeast Region |
| 148200 | 668 | Roy Creek | Green Lake | 0 | 7.18 | Medium Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | Northeast Region |
| 148300 | 543 | Wuerches Creek | Green Lake | 0 | 4.4 | Low Priority | NPS | 303d Listed, Addition | Sediment, Total Phosphorus | Degraded Habitat, Elevated Water Temperature, Low DO | Category 5A | Northeast Region |
| 900700 | 57 | Braezels Br | Green, Lafayette | 0 | 4.06 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 899500 | 206 | Jockey Hollow Creek | Green, Lafayette | 0 | 3.1 | Implementation Priority | NPS | TMDL Approved | Sediment | Degraded Habitat | Category 5C | South Central Region |
| 1211000 | 54 | Blue River | Iowa | 32.1 | 35.21 | Low Priority | NPS | 303d Listed | Sediment | Degraded Habitat | Category 5A | South Central Region |
| 928600 | 58 | Brewery Creek | Iowa | 0 | 3.32 | Low Priority | PS/NPS Blend | 303d Listed | Lead, Zinc | Chronic Aquatic Toxicity | Category 5A | South Central Region |
| 910800 | 111 | Dodge Br | Iowa | 0 |