| Red Cedar Lake | Red Cedar Lake | | | 813100 | Lake | Jefferson | Unknown Pollutant | NA | Water Delisted | Delisted 2020 |
| Unnamed | Inlet of Lake Ripley | 0.00 | 3.62 | 809700 | River | Jefferson | Total Phosphorus | Impairment Unknown | 303d Listed | Medium |
| Koshkonong Creek | Lower Koshkonong Creek | 0.00 | 27.27 | 808800 | River | Dane, Jefferson | Total Phosphorus | High Phosphorus Levels | 303d Listed | Low |
| Lake Koshkonong | Lakeland Campground Beach -- 2803 E. State Rd. 59, Lake Koshkonong | 0.00 | 0.02 | 808700 | Inland Beach | Rock | E. coli | Recreational Restrictions - Pathogens | 303d Listed | Low |
| Lake Ripley | Lake Ripley Beach | 0.00 | 0.09 | 809600 | Inland Beach | Jefferson | E. coli | Recreational Restrictions - Pathogens | 303d Listed | Low |
| Koshkonong Creek | Upper Koshkonong | 27.27 | 48.42 | 808800 | River | Dane, Jefferson | Unknown Pollutant | NA | Pollutant Removed | Delisted 2020 |
| Koshkonong Creek | Upper Koshkonong | 27.27 | 48.42 | 808800 | River | Dane, Jefferson | Total Phosphorus | High Phosphorus Levels, Degraded Biological Community | 303d Listed | Low |
| Clear Lake | Clear Lake | | | 775000 | Lake | Rock | Unknown Pollutant | Eutrophication | 303d Listed | Low |
| Clear Lake | Clear Lake | | | 775000 | Lake | Rock | Total Phosphorus | Eutrophication | Pollutant Removed | Delisted 2024 |
| Clear Lake | Clear Lake | | | 775000 | Lake | Rock | Mercury | NA | Pollutant Removed | Delisted 2020 |
| Storrs Lake | Storrs Lake | | | 780300 | Lake | Rock | Unknown Pollutant | Degraded Aquatic Vegetation | 303d Listed | Low |
| Rock River | Rock River | 193.11 | 201.29 | 788800 | River | Rock | Total Phosphorus | Low DO | TMDL Approved | Not Applicable |
| Rock River | Rock River | 193.11 | 201.29 | 788800 | River | Rock | Sediment/Total Suspended Solids | Degraded Habitat | TMDL Approved | Not Applicable |
| Rock River | Rock River | 193.11 | 201.29 | 788800 | River | Rock | PCBs | NA | Pollutant Removed | Delisted 2006 |
| Rock River | Rock River | 207.32 | 242.84 | 788800 | River | Dodge, Jefferson | Total Phosphorus | Degraded Biological Community, Low DO, Excess Algal Growth, Eutrophication | TMDL Approved | Not Applicable |
| Rock River | Rock River | 201.29 | 207.03 | 788800 | River | Rock | Total Phosphorus | Low DO | TMDL Approved | Not Applicable |
| Rock River | Rock River | 201.29 | 207.03 | 788800 | River | Rock | Sediment/Total Suspended Solids | Degraded Habitat | TMDL Approved | Not Applicable |
| Rock River | Rock River | 201.29 | 207.03 | 788800 | River | Rock | Mercury | NA | Pollutant Removed | Delisted 2006 |
| Rock River | Rock River | 201.29 | 207.03 | 788800 | River | Rock | PCBs | NA | Pollutant Removed | Delisted 2006 |
| Lake Koshkonong | Lake Koshkonong | | | 808700 | Lake | Dane, Jefferson, Rock | Sediment/Total Suspended Solids | Degraded Habitat, Turbidity | TMDL Approved | Not Applicable |
| Lake Koshkonong | Lake Koshkonong | | | 808700 | Lake | Dane, Jefferson, Rock | Total Phosphorus | Low DO, Excess Algal Growth, Eutrophication | TMDL Approved | Not Applicable |