| La Crosse River | La Crosse River | 0.00 | 17.84 | 1650200 | River | La Crosse | Total Phosphorus | Impairment Unknown | 303d Listed | Low |
| Unnamed | La Crosse River Marsh | | | 5561990 | Wetlands | La Crosse | Lead | Lead Contaminated Sediments | 303d Listed | Low |
| Unnamed | La Crosse River Marsh | | | 5562016 | Wetlands | La Crosse | Lead | Lead Contaminated Sediments | 303d Listed | Low |
| Mississippi River | Mississippi (Reach 3) LaCrosse-Pine - LD 6 to Root River (Pool 7 to upper Pool 8) | 693.70 | 714.20 | 721000 | River | La Crosse, Trempealeau | Mercury | Acute Aquatic Toxicity, Mercury Contaminated Fish Tissue, Impairment Unknown, Elevated Human Health Risks - Toxics | 303d Listed | Low |
| Mississippi River | Mississippi (Reach 3) LaCrosse-Pine - LD 6 to Root River (Pool 7 to upper Pool 8) | 693.70 | 714.20 | 721000 | River | La Crosse, Trempealeau | PCBs | PCBs Contaminated Fish Tissue, Impairment Unknown | 303d Listed | Low |
| Mississippi River | Mississippi (Reach 3) LaCrosse-Pine - LD 6 to Root River (Pool 7 to upper Pool 8) | 693.70 | 714.20 | 721000 | River | La Crosse, Trempealeau | Total Phosphorus | Impairment Unknown, Excess Algal Growth | 303d Listed | Low |
| Neshonoc Lake | Neshonoc Lake | | | 1653500 | Impoundment | La Crosse | Total Phosphorus | Excess Algal Growth, Elevated pH , Eutrophication | 303d Listed | Low |
| Neshonoc Lake | Neshonoc Lake | | | 1653500 | Impoundment | La Crosse | Mercury | Mercury Contaminated Fish Tissue | 303d Listed | Low |
| Neshonoc Lake | Neshonoc Lake | | | 1653500 | Impoundment | La Crosse | PCBs | NA | Pollutant Removed | Delisted 2012 |
| Neshonoc Lake | Neshonoc Lake | | | 1653500 | Impoundment | La Crosse | Sediment/Total Suspended Solids | Elevated pH , Eutrophication | 303d Listed | Low |
| Gill Coulee Creek | Gills Coulee Creek | 1.39 | 4.86 | 1652300 | River | La Crosse | Sediment/Total Suspended Solids | Degraded Habitat | TMDL Approved | Not Applicable |
| Gill Coulee Creek | Gills Coulee Creek | 0.00 | 1.39 | 1652300 | River | La Crosse | Sediment/Total Suspended Solids | Degraded Habitat | TMDL Approved | Not Applicable |
| Bostwick Creek | Bostwick Creek | 0.00 | 3.65 | 1650900 | River | La Crosse | Total Phosphorus | Impairment Unknown | 303d Listed | Low |