| Big Cut | Big Cut |  |  | 104.20 | RIVERINE BACKWATER | 270800 | Waupaca |  | Unknown |  |  | 
| Cedar Creek | Cedar Creek | 0.00 | 4.50 | 4.50 | RIVER | 291500 | Waupaca | 2011 | Unknown |  |  | 
| Cincoe Lake | Cincoe Lake |  |  | 180.62 | LAKE | 271100 | Waupaca | 2011 | Unknown |  |  | 
| Colic Bayou | Colic Bayou (Pickerel) |  |  | 50.88 | LAKE | 270700 | Waupaca | 2015 | Good |  |  | 
| Flynn Lake | Flynn Lake |  |  | 14.90 | LAKE | 186200 | Waupaca | 2011 | Unknown |  |  | 
| Fremont Pond | Fremont Pond |  |  | 1.44 | LAKE | 186300 | Waupaca |  | Unknown |  |  | 
| Horseshoe Bayou | Horseshoe Bayou |  |  | 14.01 | LAKE | 271900 | Waupaca |  | Unknown |  |  | 
| Jenny Bayou | Jenny Bayou |  |  | 29.35 | LAKE | 270600 | Waupaca | 2011 | Unknown |  |  | 
| Little Cut | Little Cut |  |  | 23.67 | RIVERINE BACKWATER | 271800 | Waupaca |  | Unknown |  |  | 
| Little Horseshoe Bayou | Little Horseshoe Bayou |  |  | 6.06 | LAKE | 190400 | Waupaca |  | Unknown |  |  | 
| Little Wolf River | Little Wolf River | 0.00 | 8.76 | 8.76 | RIVER | 272400 | Marathon, Portage, Waupaca | 2025 | Excellent |  | ERW | 
| Lowell Bayou | Lowell Bayou |  |  | 9.92 | LAKE | 271000 | Waupaca |  | Unknown |  |  | 
| Mill Cut | Mill Cut Creek |  |  | 14.90 | LAKE | 270900 | Waupaca |  | Unknown |  |  | 
| Miller Bayou | Millers Bayou |  |  | 17.98 | LAKE | 257100 | Waupaca | 1999 | Unknown |  |  | 
| Mouse Creek | Mouse Creek | 0.00 | 3.19 | 3.19 | RIVER | 272500 | Waupaca | 2007 | Unknown |  |  | 
| Partridge Crop Lake | Partridge Crop Lake |  |  | 276.01 | LAKE | 272000 | Waupaca | 2017 | Good |  |  | 
| Partridge Lake | Partridge Lake |  |  | 1184.96 | LAKE | 253800 | Waupaca | 2017 | Fair |  |  | 
| Potters Creek | Potters Creek | 0.00 | 7.77 | 7.77 | RIVER | 271200 | Outagamie, Waupaca | 2018 | Unknown |  |  | 
| Rat River | Rat River | 0.00 | 13.14 | 13.14 | RIVER | 251800 | Outagamie, Winnebago | 2025 | Poor |  |  | 
| Shaky Lake | Shaky Lake |  |  | 11.14 | LAKE | 271700 | Outagamie | 2011 | Unknown |  |  | 
| Shaw Landing | Shaw Landing |  |  | 1.63 | LAKE | 198500 | Waupaca |  | Unknown |  |  | 
| Templeton Bayou | Templeton Bayou |  |  | 79.13 | LAKE | 257300 | Waupaca | 2012 | Unknown |  |  | 
| Tom Bayou | Tom Bayou |  |  | 4.90 | LAKE | 200400 | Waupaca |  | Unknown |  |  | 
| Traders Bayou | Traders Bayou |  |  | 37.73 | LAKE | 200500 | Waupaca |  | Unknown |  |  | 
| Unnamed | TRIBUTARY TO THE WOLF RIVER | 0.00 | 0.92 | 0.92 | RIVER | 5020118 | Outagamie, Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water | 0.00 | 1.13 | 1.13 | RIVER | 5018976 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water | 0.00 | 1.86 | 1.86 | RIVER | 5018933 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water | 0.00 | 2.33 | 2.33 | RIVER | 272450 | Waupaca | 2018 | Unknown |  |  | 
| Unnamed | Local Water | 0.00 | 4.13 | 4.13 | RIVER | 271400 | Outagamie, Waupaca | 2015 | Fair |  |  | 
| Unnamed | Trib to the Wolf River | 0.00 | 5.84 | 5.84 | RIVER | 271300 | Outagamie, Waupaca |  | Fair |  |  | 
| Unnamed | Un Lake |  |  | 0.33 | LAKE | 204700 | Waupaca |  | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 0.77 | LAKE | 204800 | Waupaca |  | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 3.68 | LAKE | 204900 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 12.33 | RIVERINE BACKWATER | 253100 | Waupaca | 2020 | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 0.77 | LAKE | 253400 | Waupaca |  | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 4.34 | LAKE | 253700 | Waupaca |  | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 0.89 | LAKE | 291700 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.50 | LAKE | 5548229 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 4.38 | LAKE | 5549394 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.17 | LAKE | 5549421 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 7.58 | LAKE | 5549459 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.74 | LAKE | 5550026 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 4.16 | LAKE | 5550766 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 6.16 | LAKE | 5550826 | Waupaca | 2010 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.03 | LAKE | 5551023 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.03 | LAKE | 5551697 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.46 | LAKE | 5551731 | Outagamie |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.20 | LAKE | 5581216 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.79 | LAKE | 5581217 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 5.17 | LAKE | 5582177 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 12.55 | LAKE | 5582180 | Waupaca | 2015 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 19.11 | LAKE | 5582182 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.88 | LAKE | 5582469 | Winnebago |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.42 | LAKE | 5582472 | Winnebago |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 30.11 | LAKE | 5584961 | Waupaca | 2011 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 6.60 | LAKE | 5584981 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 11.59 | LAKE | 5584984 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.19 | LAKE | 5584985 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 6.92 | LAKE | 5585351 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.57 | LAKE | 5585398 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 13.71 | LAKE | 5585435 | Waupaca | 2011 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 6.15 | LAKE | 5585705 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.57 | LAKE | 5585808 | Waupaca |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.67 | LAKE | 5591199 | Waupaca |  | Unknown |  |  | 
| Wolf River | Wolf River-Main Stem | 9.45 | 42.00 | 32.55 | RIVER | 241300 | Forest, Langlade, Menominee, Oneida, Outagamie, Shawano, Waupaca, Winnebago | 2025 | Good |  |  | 
| Wolf River | Wolf River | 21.26 | 24.37 | 3.11 | RIVER | 241300 | Forest, Langlade, Menominee, Oneida, Outagamie, Shawano, Waupaca, Winnebago | 2015 | Good |  |  | 
| Wolf River - Unnamed Horseshoe | Unnamed Horseshoe of Rock River |  |  | 17.30 | RIVERINE BACKWATER | 291400 | Waupaca | 2010 | Unknown |  |  |