| Wolf River | Wolf River-Main Stem | 9.45 | 42.00 | 241300 | River | Waupaca, Winnebago | PCBs | NA | Water Delisted | Delisted 2018 |
| Unnamed | Unnamed Stream | 0.00 | 0.95 | 5020640 | River | Waupaca | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Unnamed | Unnamed Stream | 0.00 | 1.61 | 5020550 | River | Waupaca | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Unnamed | Unnamed Stream | 0.00 | 1.71 | 258000 | River | Waupaca | Total Phosphorus | Impairment Unknown | 303d Listed | Low |
| Unnamed | Unnamed Stream | 0.00 | 2.60 | 257900 | River | Waupaca | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Unnamed | Unnamed Stream | 0.00 | 2.88 | 257800 | River | Waupaca | Total Phosphorus | Impairment Unknown | TMDL Approved | Not Applicable |
| Unnamed | Unnamed Trib to Waupaca River | 0.00 | 3.37 | 5021414 | River | Waupaca | Total Phosphorus | Degraded Biological Community | TMDL Approved | Not Applicable |
| Tomorrow River | Tomorrow/Waupaca River | 18.45 | 32.30 | 270400 | River | Portage | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Pope Lake | Pope Lake | | | 262900 | Lake | Waupaca | Total Phosphorus | Impairment Unknown | 303d Listed | Low |
| Wolf Lake | Wolf Lake | | | 241100 | Lake | Portage | Total Phosphorus | Impairment Unknown | TMDL Development | High |
| Mirror Lake | Mirror Lake | | | 258700 | Lake | Waupaca | Unknown Pollutant | Degraded Aquatic Vegetation | 303d Listed | Low |
| Bear Creek | Bear Creek | 1.94 | 7.23 | 267400 | River | Portage | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Waupaca River | Waupaca River | 17.25 | 32.77 | 257400 | River | Waupaca | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Waupaca River | Tomorrow/Waupaca River | 32.77 | 38.58 | 257400 | River | Portage | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Waupaca River | Tomorrow/Waupaca River | 38.58 | 45.98 | 257400 | River | Portage | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Old Taylor Lake | Old Taylor Lake | | | 195000 | Lake | Waupaca | Total Phosphorus | High Phosphorus Levels | TMDL Approved | Not Applicable |
| Crystal River | Crystal River | 2.43 | 12.20 | 258200 | River | Waupaca | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Shadow Lake | Shadow Lake | | | 258600 | Lake | Waupaca | Unknown Pollutant | Degraded Aquatic Vegetation | 303d Listed | Low |
| Columbia Lake | Cary Millpond | | | 262400 | Lake | Waupaca | Mercury | NA | Water Delisted | Delisted 2020 |
| Hartman Creek | Hartman Creek | 0.00 | 1.61 | 263000 | River | Waupaca | Unknown Pollutant | Elevated Water Temperature | 303d Listed | Low |
| Spring Lake | Spring Lake | | | 267200 | Springs-Lake | Portage | Total Phosphorus | High Phosphorus Levels | TMDL Approved | Not Applicable |
| Mack Creek | Mack (Brown. Spring) Creek | 0.00 | 1.96 | 267300 | River | Portage | Total Phosphorus | Impairment Unknown | 303d Listed | Low |
| Collins Lake | Collins (Fish) Lake | | | 270200 | Lake | Portage | Total Phosphorus | Impairment Unknown, Excess Algal Growth | TMDL Approved | Not Applicable |
| Collins Lake | Collins (Fish) Lake | | | 270200 | Lake | Portage | Mercury | Mercury Contaminated Fish Tissue | 303d Listed | Low |