| Bensel Pond | Mississippi Backwater into Waumandee Creek |  |  | 44.80 | RIVERINE BACKWATER | 1809600 | Buffalo | 2021 | Unknown |  |  | 
| Danuser Creek | Danuser Creek | 0.00 | 7.07 | 7.07 | RIVER | 1812000 | Buffalo | 2023 | Poor | CLASS II |  | 
| Eagle Creek | Eagle Creek | 0.00 | 3.49 | 3.49 | RIVER | 1808400 | Buffalo | 2015 | Good |  |  | 
| Eagle Creek | Eagle Creek | 3.49 | 9.09 | 5.60 | RIVER | 1808400 | Buffalo | 2022 | Good | CLASS II |  | 
| Eagle Creek | Eagle Creek | 9.09 | 17.56 | 8.47 | RIVER | 1808400 | Buffalo | 2021 | Fair | CLASS II |  | 
| Fountain City Bay | Mississippi Backwater near Eagle Creek confluence | 0.00 | 4.00 | 4.00 | RIVERINE BACKWATER | 729600 | Buffalo | 2021 | Unknown |  |  | 
| Indian Point Slough | Mississippi Backwater near Indian Point Rd. |  |  | 72.84 | RIVERINE BACKWATER | 729990 | Buffalo | 2012 | Unknown |  |  | 
| Kieselhorse Bay | Kieselhorse Bay |  |  | 201.77 | LAKE | 729700 | Buffalo | 2014 | Unknown |  |  | 
| Little Waumandee Creek | Little Waumandee Creek | 0.00 | 11.00 | 11.00 | RIVER | 1810300 | Buffalo | 2021 | Poor | CLASS II |  | 
| Little Waumandee Creek | Little Waumandee Creek | 11.00 | 21.11 | 10.11 | RIVER | 1810300 | Buffalo | 2017 | Excellent | CLASS II |  | 
| Lizzie Pauls Pond | Mississippi backwater (Lizzie Pauls Pond) |  |  | 53.36 | RIVERINE BACKWATER | 1813500 | Buffalo | 2025 | Excellent |  |  | 
| Mississippi River | Mississippi (Reach 2) Buffalo-Whitewater - Chippewa River to LD 6 (lower Pool 4 to Pool 6) | 714.20 | 763.40 | 49.20 | RIVER | 721000 | Buffalo, Crawford, Grant, La Crosse, Pierce, Trempealeau, Vernon | 2025 | Poor |  |  | 
| Moseman Slough | Mississippi backwater (Moseman Slough) |  |  | 17.41 | RIVERINE BACKWATER | 730300 | Buffalo |  | Unknown |  |  | 
| Probst Lake | Mississippi backwater (Probst Lake) |  |  | 427.33 | RIVERINE BACKWATER | 730200 | Buffalo |  | Unknown |  |  | 
| Screechowl Creek | Screechowl Creek | 0.00 | 1.00 | 1.00 | RIVER | 1810100 | Buffalo |  | Unknown |  |  | 
| Spring Lake | Miss River -Pool No.6 |  |  | 373.55 | RIVERINE BACKWATER | 730100 | Buffalo |  | Unknown |  |  | 
| Unnamed | Unnamed Trib to Eagle Creek | 0.00 | 0.58 | 0.58 | RIVER | 5022082 | Buffalo | 2016 | Unknown |  |  | 
| Unnamed | Local Water | 0.00 | 0.84 | 0.84 | RIVER | 5019909 | Buffalo | 2015 | Unknown |  |  | 
| Unnamed | Unnamed Creek 28-13 | 0.00 | 2.00 | 2.00 | RIVER | 1812400 | Buffalo |  | Unknown |  |  | 
| Unnamed | Unnamed Creek 18-13 | 0.00 | 2.00 | 2.00 | RIVER | 1812900 | Buffalo |  | Unknown |  |  | 
| Unnamed | Buell Valley Creek | 0.00 | 2.32 | 2.32 | RIVER | 1813100 | Buffalo | 2015 | Poor |  |  | 
| Unnamed | Local Water | 0.00 | 2.66 | 2.66 | RIVER | 1810900 | Buffalo | 2015 | Good |  |  | 
| Unnamed | Wolf Valley Creek | 0.00 | 2.70 | 2.70 | RIVER | 1811200 | Buffalo | 2015 | Poor |  |  | 
| Unnamed | Local Water | 0.00 | 2.81 | 2.81 | RIVER | 3000034 | Buffalo | 2003 | Unknown |  |  | 
| Unnamed | Schultz Valley Creek | 0.00 | 3.00 | 3.00 | RIVER | 1810600 | Buffalo |  | Unknown |  |  | 
| Unnamed | Unnamed Creek 31-4 | 0.00 | 3.00 | 3.00 | RIVER | 1812100 | Buffalo | 1991 | Unknown |  |  | 
| Unnamed | Oak Valley Cr | 0.00 | 3.21 | 3.21 | RIVER | 1809800 | Buffalo | 2003 | Unknown |  |  | 
| Unnamed | Weiland Valley Creek | 0.00 | 3.22 | 3.22 | RIVER | 1813000 | Buffalo | 2015 | Poor |  |  | 
| Unnamed | Waters Valley Creek | 0.00 | 4.00 | 4.00 | RIVER | 1811500 | Buffalo | 2015 | Good |  |  | 
| Unnamed | Hesch Valley Creek | 0.00 | 4.00 | 4.00 | RIVER | 1811900 | Buffalo |  | Unknown |  |  | 
| Unnamed | Yeager Valley Creek | 0.00 | 4.43 | 4.43 | RIVER | 1810200 | Buffalo | 2015 | Poor | CLASS II |  | 
| Unnamed | Florin Valley Creek | 0.00 | 5.00 | 5.00 | RIVER | 1810400 | Buffalo |  | Unknown |  |  | 
| Unnamed | Cochrane Ditch (Rose Valley Cr) | 0.00 | 6.50 | 6.50 | RIVER | 1813600 | Buffalo | 2025 | Poor |  |  | 
| Unnamed | Joos Valley Creek | 0.00 | 7.44 | 7.44 | RIVER | 1808900 | Buffalo | 2015 | Fair |  |  | 
| Unnamed | Jahns Valley Creek | 0.00 | 7.71 | 7.71 | RIVER | 1810800 | Buffalo |  | Poor |  |  | 
| Unnamed | Irish Valley Creek | 0.00 | 7.89 | 7.89 | RIVER | 1811400 | Buffalo | 2015 | Poor |  |  | 
| Unnamed | Schoepp Valley Creek | 0.00 | 7.95 | 7.95 | RIVER | 1809900 | Buffalo | 2015 | Good |  |  | 
| Unnamed | Schmidt Valley Creek | 0.00 | 8.00 | 8.00 | RIVER | 1811100 | Buffalo |  | Unknown |  |  | 
| Unnamed | Cochrane Ditch (Rose Valley Cr) | 6.50 | 10.06 | 3.56 | RIVER | 1813600 | Buffalo |  | Poor |  |  | 
| Unnamed | Un Lake |  |  | 3.09 | LAKE | 1807600 | Buffalo |  | Unknown |  |  | 
| Unnamed | Un Lake |  |  | 0.13 | LAKE | 1807650 | Buffalo |  | Unknown |  |  | 
| Unnamed | Mississippi Backwater into Waumandee Creek |  |  | 157.29 | RIVERINE BACKWATER | 1809200 | Buffalo | 2016 | Fair |  |  | 
| Unnamed | Local Water |  |  | 1.05 | LAKE | 1809400 | Buffalo |  | Unknown |  |  | 
| Unnamed | Mississippi Backwater into Waumandee Creek |  |  | 76.28 | RIVERINE BACKWATER | 1809500 | Buffalo | 2016 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.10 | IMPOUNDMENT | 5551798 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 8.93 | LAKE | 5553132 | Buffalo | 2010 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.76 | LAKE | 5553339 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.08 | LAKE | 5553426 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.04 | LAKE | 5553522 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 3.47 | LAKE | 5553604 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 5.85 | LAKE | 5554221 | Buffalo | 2010 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 2.45 | LAKE | 5554347 | Buffalo |  | Unknown |  |  | 
| Unnamed | Local Water |  |  | 6.89 | LAKE | 5554418 | Buffalo |  | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 38.94 | RIVERINE BACKWATER | 5582338 | Buffalo | 2017 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 241.01 | LAKE | 5589764 | NA | 2017 | Unknown |  |  | 
| Unnamed | Local Water |  |  | 46.00 | LAKE | 5589769 | Buffalo | 2014 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 250.88 | RIVERINE BACKWATER | 5589777 | Buffalo | 2016 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 152.84 | RIVERINE BACKWATER | 5589778 | NA | 2012 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 3682.18 | LAKE | 5589779 | NA | 2017 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 24.22 | LAKE | 5589781 | NA | 2017 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 5.17 | LAKE | 5589782 | NA | 2012 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 10.11 | LAKE | 5589783 | NA | 2017 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 37.25 | LAKE | 5589785 | NA | 2017 | Unknown |  |  | 
| Unnamed | Unnamed Lake |  |  | 310.09 | RIVERINE BACKWATER | 5589818 | NA | 2017 | Unknown |  |  | 
| Waumandee Creek | Waumandee Creek | 0.00 | 12.38 | 12.38 | RIVER | 1808300 | Buffalo | 2021 | Poor |  |  | 
| Waumandee Creek | Waumandee Creek | 26.72 | 33.64 | 6.92 | RIVER | 1808300 | Buffalo | 2022 | Fair | CLASS II |  |