| Lake Michigan | Lake Michigan | 0.00 | 261.05 | 20 | Great Lakes Shoreline | Door, Kenosha, Kewaunee, Manitowoc, Milwaukee, Ozaukee, Racine, Sheboygan | Mercury | Mercury Contaminated Fish Tissue | 303d Listed | Low |
| Lake Michigan | Lake Michigan | 0.00 | 261.05 | 20 | Great Lakes Shoreline | Door, Kenosha, Kewaunee, Manitowoc, Milwaukee, Ozaukee, Racine, Sheboygan | PCBs | PCBs Contaminated Fish Tissue | 303d Listed | Low |
| Silver Creek | Silver Creek | 8.70 | 17.98 | 67300 | River | Manitowoc | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Unnamed | Unnamed Trib to Fourmile Creek | 0.00 | 1.52 | 64800 | River | Sheboygan | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Centerville Creek | Centerville Creek | 0.00 | 5.54 | 65400 | River | Manitowoc | Total Phosphorus | High Phosphorus Levels | TMDL Approved | Not Applicable |
| Silver Lake | Silver Lake | | | 67400 | Lake | Manitowoc | Total Phosphorus | Fish Kills, Excess Algal Growth, Eutrophication | TMDL Approved | Not Applicable |
| Lake Michigan | Fischer Park Beaches, Lake Michigan | 0.00 | 0.85 | 20 | Great Lakes Beach | Manitowoc | E. coli | Recreational Restrictions - Pathogens | 303d Listed | Low |
| Lake Michigan | Hika Park Bay Beach, Lake Michigan | 0.00 | 0.20 | 20 | Great Lakes Beach | Manitowoc | E. coli | Recreational Restrictions - Pathogens | 303d Listed | Low |
| Calvin Creek | Calvin Creek | 0.00 | 5.83 | 66900 | River | Manitowoc | Total Phosphorus | Degraded Biological Community | TMDL Approved | Not Applicable |
| Pine Creek | Pine Creek | 2.00 | 6.00 | 66300 | River | Manitowoc | Total Phosphorus | NA | Water Delisted | Delisted 2020 |
| Carstens Lake | Carstens Lake | | | 66800 | Lake | Manitowoc | Total Phosphorus | Excess Algal Growth, Degraded Aquatic Vegetation, Eutrophication | TMDL Approved | Not Applicable |
| Gass Lake | Gass Lake | | | 67100 | Lake | Manitowoc | Total Phosphorus | High Phosphorus Levels, Excess Algal Growth | TMDL Approved | Not Applicable |
| Hartlaub Lake | Hartlaub Lake | | | 67200 | Lake | Manitowoc | Total Phosphorus | Impairment Unknown, Excess Algal Growth | TMDL Approved | Not Applicable |
| Silver Creek | Silver Creek | 0.00 | 8.44 | 67300 | River | Manitowoc | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| English Lake | English Lake | | | 68100 | Lake | Manitowoc | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Weyers Lake | Weyers Lake | | | 49400 | Lake | Manitowoc | Total Phosphorus | High Phosphorus Levels, Excess Algal Growth | TMDL Approved | Not Applicable |
| Sevenmile Creek | Sevenmile Creek | 0.00 | 5.00 | 65100 | River | Sheboygan | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Fischer Creek | Fischer Creek | 0.00 | 8.78 | 65800 | River | Manitowoc | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Point Creek | Point Creek | 0.00 | 13.74 | 66000 | River | Manitowoc | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |