| Ahnapee River | 14.7 | 15 |
| Alder Creek (Little Jump River tributary) | 21.1 | 21 |
| Alder Creek (Pine River (Wolf River tributary)) | 15.8 | 16 |
| Allen Creek | 27.1 | 27 |
| Amnicon River | 45.5 | 59 |
| Apple Creek | 24.2 | 24 |
| Apple River (Mississippi River tributary) | 4.9 | 8 |
| Apple River (St. Croix River tributary) | 77.7 | 112 |
| Apple River - West Fork (Mississippi River tributary) | 2.9 | 3 |
| Armstrong Creek | 17 | 17 |
| Arrowhead River | 12.5 | 13 |
| Ashippun River | 33.2 | 33 |
| Bad Axe River | 4 | 64 |
| Bad Axe River - North Fork | 31.4 | 44 |
| Bad Axe River - South Fork | 15.9 | 16 |
| Bad Axe River - Springville Branch | 12.8 | 13 |
| Bad River | 76.2 | 389 |
| Balsam Creek | 22.3 | 22 |
| Baraboo River | 116.5 | 171 |
| Baraboo River - West Branch | 15.8 | 16 |
| Bark River | 69.5 | 88 |
| Bass Creek | 19.8 | 20 |
| Bean Brook | 18.6 | 19 |
| Bear Creek (Chippewa River tributary) | 18 | 18 |
| Bear Creek (Embarrass River tributary) | 15.3 | 15 |
| Bear Creek (Wisconsin River tributary) | 27 | 27 |
| Bear Creek (Wolf River (Fox River (Lake Michigan tributary))) | 18.9 | 19 |
| Bear River | 22.6 | 23 |
| Bears Grass Creek | 16 | 16 |
| Beartrap Creek | 23.1 | 23 |
| Beaver Brook | 11.4 | 34 |
| Beaver Brook - North Branch | 12.9 | 13 |
| Beaver Brook - South Branch | 10 | 10 |
| Beaver Creek (Black River (Mississippi River tributary)) | 17.9 | 51 |
| Beaver Creek (Lemonweir River tributary) | 21.9 | 22 |
| Beaver Creek - North Branch (Peshtigo River tributary) | 11.9 | 12 |
| Beaver Creek - North Fork (Black River (Mississippi River tributary)) | 19.5 | 20 |
| Beaver Creek (Peshtigo River tributary) | 3.5 | 32 |
| Beaver Creek - South Branch (Peshtigo River tributary) | 16.5 | 17 |
| Beaver Creek - South Fork (Black River (Mississippi River tributary)) | 13.6 | 14 |
| Beaver Dam River | 43 | 59 |
| Big Drywood Creek | 17.9 | 18 |
| Big Eau Pleine River | 45.9 | 106 |
| Big Eau Pleine River - East Branch | 11.4 | 11 |
| Big Eau Pleine River - West Branch | 12.3 | 12 |
| Big Green River | 15.3 | 15 |
| Big Hay Meadow Creek | 23.6 | 24 |
| Big Rib River | 61 | 124 |
| Big River | 12.8 | 13 |
| Big Roche a Cri Creek | 48.7 | 49 |
| Big Sandy Creek | 19 | 19 |
| Big Weirgor Creek | 21.3 | 36 |
| Billings Creek | 15.2 | 15 |
| Black Creek | 27.7 | 28 |
| Black Creek | 23.1 | 23 |
| Black Earth Creek | 27.1 | 27 |
| Black River - East Fork (Mississippi River tributary) | 57.5 | 77 |
| Black River (Lake Superior tributary) | 2.1 | 2 |
| Black River (Mississippi River tributary) | 192 | 691 |
| Black River (Nemadji River tributary) | 36.6 | 37 |
| Blake Fork | 17.2 | 17 |
| Blue Mounds Creek | 11.1 | 38 |
| Blue River | 35.3 | 62 |
| Bluff Creek | 18.2 | 18 |
| Boice Creek | 15.9 | 16 |
| Bois Brule River | 43.9 | 44 |
| Bonner Branch | 18.3 | 18 |
| Bostwick Creek | 16.2 | 16 |
| Bower Creek | 15.7 | 16 |
| Branch River | 36.9 | 37 |
| Bridge Creek | 21 | 21 |
| Brule River | 52.3 | 52 |
| Brunet River | 40.4 | 58 |
| Brunsweiler River | 30 | 30 |
| Buffalo River | 70.1 | 119 |
| Buffalo River - North Fork | 15.6 | 16 |
| Buffalo River - South Fork | 16.4 | 16 |
| Bull Junior Creek | 18.9 | 19 |
| Butternut Creek | 33.5 | 34 |
| Cady Creek | 16.1 | 16 |
| Carter Creek | 25.1 | 25 |
| Cedar Creek | 32.7 | 33 |
| Chaffee Creek | 15.9 | 16 |
| Chase Creek | 3.9 | 20 |
| Chases Brook | 26.2 | 26 |
| Chippewa River | 196.2 | 2,858 |
| Chippewa River - East Fork | 84.6 | 117 |
| Chippewa River - West Fork | 37.3 | 90 |
| Clam River | 64 | 128 |
| Clam River - North Fork | 44 | 64 |
| Comet Creek | 26.7 | 27 |
| Coon Creek | 37.7 | 38 |
| Copper River | 9 | 50 |
| Copper River - Middle Fork | 11.3 | 11 |
| Copper River - North Fork | 21.9 | 22 |
| Copper River - South Fork | 7.5 | 19 |
| Couderay River | 19.3 | 19 |
| Crawfish River | 76.9 | 213 |
| Crawfish River - North Branch | 30.6 | 31 |
| Crazy Horse Creek | 17.4 | 17 |
| Cunningham Creek | 21.9 | 22 |
| Deerskin River | 21.4 | 21 |
| Deer Tail Creek | 39.7 | 40 |
| Denomie Creek | 15.3 | 15 |
| Des Plaines River | 22.2 | 22 |
| Devils Creek | 21.9 | 22 |
| Devils River | 15.8 | 16 |
| Dill Creek | 20.2 | 20 |
| Dodge Branch | 22.8 | 23 |
| Dougherty Creek | 16.7 | 17 |
| Douglas Creek | 19.4 | 19 |
| Dryden Creek | 16.5 | 17 |
| Drywood Creek | 3.4 | 43 |
| Duck Creek (Lake Michigan tributary) | 41.7 | 42 |
| Duck Creek - Middle Branch (Wisconsin River tributary) | 15.3 | 15 |
| Duck Creek - North Branch (Wisconsin River tributary) | 25.9 | 26 |
| Duck Creek (Wisconsin River tributary) | 16.6 | 17 |
| Duck Creek (Wisconsin River tributary) | 13.5 | 55 |
| Duncan Creek | 30.7 | 31 |
| Eagle Creek (Peshtigo River tributary) | 19.6 | 20 |
| Eagle Creek (Waumandee Creek tributary) | 17.1 | 17 |
| East Fork Iron River | 16.9 | 17 |
| East River | 42.4 | 58 |
| East Torch River | 11.3 | 11 |
| East Twin River | 41.1 | 93 |
| Eau Claire River (Chippewa River tributary) | 41.3 | 285 |
| Eau Claire River - East Branch (Wisconsin River tributary) | 29.4 | 29 |
| Eau Claire River - North Fork (Chippewa River tributary) | 54.4 | 86 |
| Eau Claire River - South Fork (Chippewa River tributary) | 48.9 | 49 |
| Eau Claire River (St. Croix River tributary) | 26.1 | 26 |
| Eau Claire River - West Branch (Wisconsin River tributary) | 28.2 | 28 |
| Eau Claire River (Wisconsin River tributary) | 42.5 | 139 |
| Eau Galle River | 51.4 | 85 |
| Eighteenmile Creek | 16.4 | 16 |
| Elk Creek | 16.4 | 16 |
| Elk Creek (Chippewa River tributary) | 25.4 | 25 |
| Elk Creek (Trempealeau River tributary) | 21.6 | 22 |
| Elk River | 43.5 | 63 |
| Embarrass River | 62 | 271 |
| Embarrass River - Middle Branch | 50 | 50 |
| Embarrass River - North Branch | 34.8 | 35 |
| Embarrass River - South Branch | 35.1 | 35 |
| Evergreen River | 21 | 21 |
| Fennimore Fork | 26.3 | 26 |
| Fenwood Creek | 16.1 | 16 |
| Fish Creek | 0.9 | 52 |
| Fisher River | 32.9 | 33 |
| Fivemile Creek | 16.8 | 17 |
| Flag River | 14.6 | 15 |
| Flambeau River | 127.2 | 562 |
| Flambeau River - South Fork | 71.3 | 221 |
| Fleming Creek | 19.6 | 20 |
| Flume Creek | 24.2 | 24 |
| Fond du Lac River | 1.5 | 46 |
| Fond Du Lac River - East Branch | 22.7 | 23 |
| Fond Du Lac River - West Branch | 21.3 | 21 |
| Fox River (Illinois River tributary) | 83.3 | 188 |
| Fox River (Lake Michigan tributary) | 198.9 | 1,837 |
| Frog Creek | 18.3 | 18 |
| Galena River | 34.8 | 37 |
| Galena River - East Fork | 1.8 | 2 |
| Gordon Creek | 22.4 | 22 |
| Grand River | 42.2 | 42 |
| Grant River | 44.9 | 115 |
| Halls Creek | 25.9 | 41 |
| Halls Creek - East Fork | 15.1 | 15 |
| Hay Creek | 27 | 46 |
| Hay River | 64.7 | 140 |
| Hay River - South Fork | 34.2 | 52 |
| Hemlock Creek | 37.9 | 38 |
| Hobbles Creek | 19.7 | 20 |
| Honey Creek - North Branch (Wisconsin River tributary) | 15.8 | 16 |
| Honey Creek (Pecatonica River tributary) | 15.6 | 16 |
| Honey Creek (White River (Fox River (Illinois River tributary))) | 28.7 | 56 |
| Honey Creek (Wisconsin River tributary) | 34.2 | 50 |
| Hunting River | 18 | 18 |
| Iron River | 11.3 | 11 |
| Iron River | 28.4 | 45 |
| Isabelle Creek | 19.4 | 19 |
| Jersey City Flowage | 5.5 | 142 |
| Johnson Creek | 17.4 | 17 |
| Johnson Creek | 20.7 | 21 |
| Jump River | 32.8 | 361 |
| Jump River - North Fork | 33.6 | 53 |
| Jump River - South Fork | 50.8 | 119 |
| Kelly Brook | 25.6 | 26 |
| Kenyon Creek | 17.8 | 18 |
| Kewaunee River | 27.9 | 43 |
| Kickapoo River | 129.1 | 186 |
| Kickapoo River - West Fork | 27 | 27 |
| Killsnake River | 19.7 | 20 |
| Kinnickinnic River | 41.4 | 41 |
| Knapp Creek | 29.1 | 29 |
| Koshkonong Creek | 54.5 | 55 |
| Kummel Creek | 18 | 18 |
| La Crosse River | 61.5 | 100 |
| Lemonweir River | 56.4 | 145 |
| Lemonweir River - East Fork | 19 | 19 |
| Lemonweir River - South Fork | 22.1 | 22 |
| Lily River | 15.3 | 15 |
| Little Amnicon River | 13.8 | 14 |
| Little Baraboo River | 19.8 | 20 |
| Little Black River | 7.1 | 34 |
| Little Black River - East Branch | 13.8 | 14 |
| Little Black River - West Branch | 13.4 | 13 |
| Little Drywood Creek | 21.2 | 21 |
| Little Eau Claire River | 29.1 | 47 |
| Little Eau Pleine River | 58.8 | 59 |
| Little Elk River | 15.7 | 16 |
| Little Grant River | 15.5 | 16 |
| Little Jump River | 33.3 | 72 |
| Little LaCrosse River | 22.7 | 23 |
| Little Lemonweir River | 25.5 | 26 |
| Little Mackay Creek | 4.4 | 20 |
| Little Menominee River | 4.9 | 5 |
| Little Peshtigo River | 18.4 | 18 |
| Little Pine Creek | 14.9 | 15 |
| Little Platte River | 41.9 | 42 |
| Little Popple River | 14.3 | 14 |
| Little Popple River | 19.2 | 19 |
| Little Rib River | 22 | 22 |
| Little Rice River | 22.1 | 22 |
| Little Richard Creek | 8.2 | 8 |
| Little River | 14.7 | 55 |
| Little River - North Branch | 14.7 | 15 |
| Little Roche a Cri Creek | 19.8 | 45 |
| Little Somo River | 20.1 | 20 |
| Little Suamico River | 23.8 | 24 |
| Little Sugar River | 31.1 | 31 |
| Little Thornapple River | 19.6 | 20 |
| Little Turtle Creek | 16.1 | 16 |
| Little Waumandee Creek | 21 | 21 |
| Little Weirgor Creek | 14.9 | 15 |
| Little West Branch Creek | 20.2 | 20 |
| Little Wolf River | 67.4 | 193 |
| Little Wolf River - North Branch | 16.7 | 17 |
| Little Wolf River - South Branch | 42.2 | 59 |
| Little Yellow River | 28.9 | 43 |
| Little Yellow River - East Branch | 14 | 14 |
| Long Lake Branch | 28.2 | 45 |
| Loon Creek | 18.6 | 19 |
| Lower Pine Creek | 28 | 28 |
| Lowes Creek | 24.4 | 24 |
| Lunch Creek | 18.5 | 19 |
| Magee Creek | 16.1 | 16 |
| Main Creek | 21.1 | 84 |
| Main Creek - Middle Fork | 16.6 | 17 |
| Main Creek - North Fork | 14.1 | 14 |
| Main Creek - South Fork | 32.3 | 32 |
| Manitowish River | 44.9 | 78 |
| Manitowoc River | 35.8 | 171 |
| Manitowoc River - North Branch | 22.3 | 22 |
| Manitowoc River - South Branch | 36.6 | 56 |
| Marengo River | 53.4 | 83 |
| Marsh Creek | 15.3 | 15 |
| Maunesha River | 30.8 | 46 |
| McCann Creek | 16 | 16 |
| McCaslin Brook | 26.3 | 26 |
| McKenzie Creek | 16.8 | 17 |
| Meadows Creek | 3.2 | 20 |
| Mecan River | 38.6 | 55 |
| Meeme River | 11.9 | 12 |
| Menominee River (Lake Michigan tributary) | 116.3 | 549 |
| Menominee River (Mississippi River tributary) | 5.1 | 5 |
| Menomonee River | 30.2 | 30 |
| Middle River | 34.3 | 34 |
| Mill Creek (Embarrass River tributary) | 22.7 | 23 |
| Mill Creek (Wisconsin River tributary) | 29.8 | 30 |
| Mill Creek (Wisconsin River tributary) | 46.9 | 47 |
| Mill Creek (Wisconsin River tributary) | 33.6 | 34 |
| Miller Creek | 16.4 | 16 |
| Milwaukee River | 103.3 | 237 |
| Milwaukee River - East Branch | 21.4 | 21 |
| Milwaukee River - North Branch | 27.9 | 28 |
| Milwaukee River - West Branch | 21.3 | 21 |
| Mineral Point Branch | 24.6 | 42 |
| Mississippi River | 233.9 | 10,552 |
| Missouri Creek | 17.9 | 18 |
| Moccasin Creek | 19.1 | 19 |
| Mondeaux River | 21.7 | 22 |
| Monico Creek | 19.4 | 19 |
| Montello River | 14.6 | 15 |
| Montreal River (Gogebic County, MI) | 53.5 | 80 |
| Montreal River - West Fork | 26.1 | 26 |
| Moose Ear Creek | 22.6 | 23 |
| Moose River (Chippewa River - West Fork tributary) | 35.2 | 35 |
| Moose River (St. Croix River tributary) | 19.1 | 19 |
| Mormon Creek | 16.3 | 16 |
| Morrison Creek | 29.1 | 29 |
| Mud Creek | 20 | 20 |
| Muddy Creek | 25 | 25 |
| Mukwonago River | 0 | 0 |
| Mullet River | 39.6 | 40 |
| Muskrat Creek | 18.5 | 19 |
| Namekagon River | 101.7 | 281 |
| Neenah Creek | 38.5 | 39 |
| Nemadji River | 35.7 | 96 |
| Nemadji River - South Fork | 1.4 | 1 |
| Neshota River | 17.2 | 17 |
| New Wood River | 17.3 | 17 |
| Nippersink Creek - North Branch | 9.5 | 10 |
| Noisy Creek | 15.5 | 16 |
| North Fish Creek | 25.4 | 25 |
| Oconomowoc River | 40.6 | 41 |
| Oconto River | 56.9 | 344 |
| Oconto River - First South Branch | 23.3 | 23 |
| Oconto River - North Branch | 69.1 | 95 |
| Oconto River - Second South Branch | 12.8 | 13 |
| Oconto River - South Branch | 54.7 | 109 |
| O'Neil Creek | 28 | 44 |
| O'Neill Creek | 3.2 | 41 |
| O'Neill Creek - North Branch | 19.9 | 20 |
| O'Neill Creek - South Branch | 18.1 | 18 |
| Onion River | 36.8 | 37 |
| Otter Creek (Eau Claire River (Chippewa River tributary)) | 26.6 | 27 |
| Otter Creek - North Branch (Sugar River tributary) | 0 | 0 |
| Otter Creek (Pecatonica River tributary) | 20.7 | 21 |
| Otter Creek (Peshtigo River tributary) | 22 | 22 |
| Otter Creek (Rock River tributary) | 17.7 | 18 |
| Otter Creek (Wisconsin River tributary) | 20.1 | 20 |
| Otter Creek (Wisconsin River tributary) | 25.5 | 26 |
| Otter Creek (Yellow River (Chippewa River tributary)) | 17.4 | 17 |
| Ounce River | 25.2 | 25 |
| Paint Creek | 24 | 24 |
| Pecatonica River | 100 | 556 |
| Pecatonica River - East Branch | 62.5 | 151 |
| Pecore Creek | 17.9 | 18 |
| Pelican River | 32.6 | 64 |
| Pelican River - North Branch | 11.7 | 12 |
| Pemebonwon River | 6.1 | 67 |
| Pemebonwon River - North Branch | 29.3 | 29 |
| Pemebonwon River - South Branch | 31.1 | 31 |
| Pensaukee River | 48.2 | 68 |
| Pensaukee River - North Branch | 20 | 20 |
| Peshtigo Brook | 28.2 | 28 |
| Peshtigo River | 136 | 335 |
| Peshtigo River - Middle Branch | 12.7 | 13 |
| Peshtigo River - North Branch | 18.9 | 19 |
| Pewaukee River | 12.1 | 12 |
| Pigeon Creek | 21.7 | 22 |
| Pigeon River (Embarrass River tributary) | 10.7 | 51 |
| Pigeon River (Lake Michigan tributary) | 31.9 | 44 |
| Pigeon River - North Branch (Embarrass River tributary) | 16.3 | 16 |
| Pigeon River - South Branch (Embarrass River tributary) | 24 | 24 |
| Pike River | 15.8 | 91 |
| Pike River | 18 | 18 |
| Pike River - Little South Branch | 15.6 | 16 |
| Pike River - North Branch | 33.5 | 34 |
| Pike River - South Branch | 25.9 | 42 |
| Pine Creek (Black River (Mississippi River tributary)) | 20.3 | 20 |
| Pine Creek (Flambeau River tributary) | 18.7 | 19 |
| Pine River (Menominee River (Lake Michigan tributary)) | 80.1 | 175 |
| Pine River - North Branch (Menominee River tributary) | 16.6 | 17 |
| Pine River - North Branch (Wisconsin River tributary) | 16.5 | 17 |
| Pine River - West Branch (Wisconsin River tributary) | 12.8 | 13 |
| Pine River (Wisconsin River tributary) | 52.3 | 92 |
| Pine River (Wisconsin River tributary) | 23.6 | 40 |
| Pine River (Wolf River tributary) | 41.6 | 102 |
| Piscasaw Creek | 4 | 4 |
| Platte River | 48.2 | 90 |
| Plover River | 62.8 | 63 |
| Plum Creek (Chippewa River tributary) | 28.7 | 29 |
| Plum Creek (Fox River (Lake Michigan tributary)) | 19.6 | 20 |
| Pokegama Creek | 18.4 | 18 |
| Pokegama River | 24.3 | 24 |
| Poplar River | 27.1 | 27 |
| Popple River (Black River (Mississippi River tributary)) | 13.6 | 58 |
| Popple River - North Fork (Black River (Mississippi River tributary)) | 25.4 | 25 |
| Popple River (Pine River (Menominee River tributary)) | 46.4 | 78 |
| Popple River - South Fork (Black River (Mississippi River tributary)) | 19.4 | 19 |
| Potato Creek | 15.5 | 16 |
| Potato River | 37 | 56 |
| Prairie River | 51.1 | 75 |
| Pratt Creek | 15.8 | 16 |
| Presque Isle River - East Branch | 7.6 | 8 |
| Presque Isle River - South Branch | 5.1 | 5 |
| Price Creek | 17.1 | 17 |
| Puchyan River | 16.7 | 17 |
| Raccoon Creek (Pecatonica River tributary) | 11.2 | 11 |
| Rat River (Peshtigo River tributary) | 36.9 | 37 |
| Rat River (Wolf River (Fox River (Lake Michigan tributary))) | 24.9 | 25 |
| Rattlesnake Creek | 21.1 | 21 |
| Red Cedar River | 101.1 | 442 |
| Red River | 43.5 | 90 |
| Red River - West Branch | 29.6 | 30 |
| Reefer Creek | 15.9 | 16 |
| Rice Creek | 15.4 | 15 |
| Rice River Flowage | 4.2 | 26 |
| Robinson Creek | 26.4 | 26 |
| Rock Creek (Black River (Mississippi River tributary)) | 20.5 | 21 |
| Rock Creek (Chippewa River tributary) | 16.3 | 16 |
| Rock River | 133.6 | 1,503 |
| Rock River - East Branch | 44.9 | 63 |
| Rock River - South Branch | 19.7 | 20 |
| Rock River - West Branch | 38.3 | 58 |
| Rocky Creek | 18 | 18 |
| Rocky Run (Black River - East Fork (Mississippi River tributary)) | 19.7 | 20 |
| Rocky Run (Wisconsin River tributary) | 24.2 | 24 |
| Root River | 43.7 | 44 |
| Rowan Creek | 19.2 | 19 |
| Rubicon River | 32.2 | 32 |
| Rush Creek | 15.7 | 16 |
| Rush River | 50.9 | 51 |
| Sailor Creek | 16.7 | 17 |
| Sand Creek | 20.4 | 20 |
| Sand River | 17.6 | 18 |
| Sauk Creek | 15.6 | 16 |
| Saunders Creek | 16.9 | 17 |
| Scarboro Creek | 15 | 15 |
| Scotch Creek | 18.3 | 18 |
| Scuppernong River | 18.9 | 19 |
| Seeley Creek | 18.5 | 19 |
| Sheboygan River | 80.6 | 157 |
| Shioc River | 28 | 85 |
| Shioc River - East Branch | 14.5 | 15 |
| Shioc River - West Branch | 15.1 | 15 |
| Silver Creek (Jump River - South Fork tributary) | 27 | 27 |
| Silver Creek (Lake Michigan tributary) | 18 | 18 |
| Silver Creek (Rock River tributary) | 16.2 | 16 |
| Sinsinawa River | 10.5 | 11 |
| Sioux River | 16.9 | 17 |
| Siskiwit River | 13.7 | 14 |
| Skinner Creek | 24.6 | 37 |
| Skinner Creek - North Fork | 12.4 | 12 |
| Soft Maple Creek | 23.7 | 24 |
| Somo River | 30.2 | 50 |
| South Fish Creek | 25.2 | 25 |
| Spafford Creek | 8.6 | 9 |
| Spirit River | 30.4 | 43 |
| Spirit River - North Fork | 12.8 | 13 |
| Spring Brook | 20.1 | 20 |
| Spring Creek | 17.1 | 17 |
| Spruce River | 21.1 | 21 |
| Squaw Creek | 15.9 | 16 |
| Squirrel River | 17.4 | 17 |
| St. Croix River | 173.1 | 1,128 |
| St. Louis River | 15.3 | 40 |
| Stony Brook | 15.5 | 16 |
| Stony Creek | 16 | 16 |
| Stuntz Brook | 17.3 | 17 |
| Suamico River | 15.9 | 16 |
| Sucker Creek | 17.7 | 18 |
| Sudan Branch | 17.7 | 18 |
| Sugar Creek | 26.8 | 27 |
| Sugar River | 83.5 | 181 |
| Sugar River - West Branch | 22.1 | 22 |
| Swamp Creek (Flambeau River tributary) | 21.9 | 22 |
| Swamp Creek (Wolf River (Fox River (Lake Michigan tributary))) | 22.7 | 23 |
| Tainter Creek | 15.1 | 15 |
| Tamarack Creek | 22.8 | 23 |
| Taylor Creek | 16.7 | 17 |
| Thornapple River | 67.1 | 87 |
| Thunder River | 7.8 | 22 |
| Thunder River - North Fork | 14 | 14 |
| Tiffany Creek | 17.6 | 18 |
| Tomahawk River | 71.2 | 137 |
| Tomorrow River | 22.1 | 22 |
| Torch River | 6.6 | 18 |
| Totagatic River | 80 | 124 |
| Trade River | 50.9 | 65 |
| Trade River - North Fork | 13.6 | 14 |
| Trappe River | 25.3 | 25 |
| Trempealeau River | 82.6 | 160 |
| Trempealeau River - North Branch | 11.4 | 11 |
| Trimbelle River | 29.4 | 29 |
| Trout Creek | 15 | 15 |
| Trout River | 17.3 | 17 |
| Turtle Creek (Hay River tributary) | 23.6 | 24 |
| Turtle Creek (Rock River tributary) | 42 | 58 |
| Turtle River | 39 | 39 |
| Tyler Forks | 36 | 36 |
| Upper Pine Creek | 18.7 | 19 |
| Upper Tamarack River | 22.2 | 43 |
| Vaughn Creek | 18.5 | 19 |
| Vermillion River | 15.4 | 15 |
| Walla Walla Creek | 17.3 | 17 |
| Waumandee Creek | 34.2 | 72 |
| Waupaca River | 44.8 | 67 |
| Wausaukee River | 29.7 | 30 |
| Wedges Creek | 24.7 | 42 |
| West Twin River | 18.4 | 51 |
| Whitcomb Creek | 15.8 | 16 |
| White River (Bad River tributary) | 66.9 | 112 |
| White River (Fox River (Illinois River tributary)) | 27.7 | 83 |
| White River (Fox River (Lake Michigan tributary)) | 35.4 | 72 |
| Willow Creek (Pine River (Wisconsin River tributary)) | 27.1 | 27 |
| Willow Creek (Pine River (Wolf River tributary)) | 44.2 | 44 |
| Willow River - South Fork (St. Croix River tributary) | 15.1 | 15 |
| Willow River (St. Croix River tributary) | 61.7 | 77 |
| Willow River (Tomahawk River tributary) | 21.6 | 22 |
| Wilson Creek | 22.8 | 23 |
| Wisconsin River | 435.8 | 2,961 |
| Wolf River (Eau Claire River - North Fork (Chippewa River tributary)) | 31.4 | 31 |
| Wolf River (Fox River (Lake Michigan tributary)) | 228.1 | 1,253 |
| Wolf River - Little West Branch (Fox River (Lake Michigan tributary)) | 17.4 | 17 |
| Wolf River - West Branch (Fox River (Lake Michigan tributary)) | 29.5 | 67 |
| Wood River | 47.8 | 48 |
| Woods Creek | 17.2 | 17 |
| Yahara River | 62.5 | 63 |
| Yellow River (Chippewa River tributary) | 69.3 | 164 |
| Yellow River - North Fork (Chippewa River tributary) | 21.3 | 21 |
| Yellow River (Red Cedar River tributary) | 39.7 | 55 |
| Yellow River - South Branch (Wisconsin River tributary) | 17.4 | 17 |
| Yellow River - South Fork (Chippewa River tributary) | 13.2 | 13 |
| Yellow River (St. Croix River tributary) | 69.4 | 88 |
| Yellow River (Wisconsin River tributary) | 96.1 | 169 |
| Yellowstone River | 26.1 | 26 |