| Alkali Creek (Belle Fourche River tributary) | 67.7 | 68 |
| Alkali Creek (Elk Creek tributary) | 19.1 | 19 |
| Alkali Creek (Moreau River - South Fork tributary) | 16.2 | 16 |
| American Creek | 14.1 | 14 |
| American Crow Creek | 32 | 50 |
| American Crow Creek - North Fork | 18.2 | 18 |
| American Horse Creek | 41.8 | 42 |
| Antelope Creek (Battle Creek (Moreau River - South Fork tributary)) | 22.6 | 23 |
| Antelope Creek (Elk Creek tributary) | 32.9 | 33 |
| Antelope Creek (Keya Paha River tributary) | 51.5 | 52 |
| Antelope Creek (Little Missouri River tributary) | 14.5 | 15 |
| Antelope Creek (Missouri River tributary) | 35.4 | 49 |
| Antelope Creek (Rabbit Creek tributary) | 71.4 | 71 |
| Antelope Creek (Rapid Creek tributary) | 19.5 | 20 |
| Archambault Creek | 15.9 | 16 |
| Arnett Creek | 15.5 | 16 |
| Artichoke Creek | 53.8 | 54 |
| Ash Creek (Bad River tributary) | 17.7 | 18 |
| Ash Creek (Bad River tributary) | 25.7 | 26 |
| Ash Creek (Cherry Creek tributary) | 22.7 | 69 |
| Ash Creek (Cheyenne River tributary) | 40.7 | 41 |
| Ash Creek - East Branch (Cherry Creek tributary) | 19.5 | 20 |
| Ash Creek (Hat Creek tributary) | 15.7 | 16 |
| Ash Creek (Vermillion River tributary) | 16.5 | 17 |
| Ash Creek - West Branch (Cherry Creek tributary) | 27.2 | 27 |
| Bachelor Creek | 25.5 | 26 |
| Bad Horse Creek | 15 | 15 |
| Badlands Creek | 4.7 | 35 |
| Bad River | 156.9 | 1,492 |
| Bad River - North Fork | 50.9 | 141 |
| Bad River - South Fork | 36.1 | 203 |
| Baptist Creek | 14.5 | 15 |
| Battle Creek (Cheyenne River tributary) | 81.2 | 127 |
| Battle Creek (Moreau River - South Fork tributary) | 41.6 | 98 |
| Bean Blossom Creek | 18.5 | 19 |
| Bear Butte Creek | 65.3 | 100 |
| Bear Creek (Cheyenne River tributary) | 24.1 | 24 |
| Bear Creek (Moreau River tributary) | 25.2 | 100 |
| Bear Creek (Niobrara River tributary) | 2.6 | 3 |
| Bear-in-the-Lodge Creek | 105.3 | 179 |
| Beaver Creek (Beaver Dam Creek - Middle Branch tributary) | 19.2 | 19 |
| Beaver Creek (Big Sioux River tributary) | 49.4 | 49 |
| Beaver Creek (Cheyenne River tributary) | 16 | 42 |
| Beaver Creek (Cheyenne River tributary) | 52.5 | 53 |
| Beaver Creek (Crow Creek (Redwater River tributary)) | 17.8 | 18 |
| Beaver Creek - East Fork (Moreau River tributary) | 14.4 | 14 |
| Beaver Creek (James River tributary) | 49 | 49 |
| Beaver Creek (Moreau River tributary) | 10.9 | 25 |
| Beaver Creek (Split Rock Creek tributary) | 16.8 | 17 |
| Beaver Dam Creek | 17.9 | 98 |
| Beaver Dam Creek - East Branch | 26.4 | 26 |
| Beaver Dam Creek - Middle Branch | 19.4 | 39 |
| Beaver Dam Creek - West Branch | 15.5 | 16 |
| Beaver Trap Creek | 15.4 | 15 |
| Beef Creek | 17.4 | 17 |
| Belle Fourche River | 191.6 | 1,644 |
| Beverly Creek | 19.4 | 19 |
| Big Buffalo Creek | 25.7 | 26 |
| Big Coulee Creek | 15.1 | 15 |
| Big Hollow Creek | 31.2 | 31 |
| Big Meadow Creek | 17 | 17 |
| Big Nasty Creek | 79.3 | 96 |
| Big Prairie Dog Creek | 39.6 | 40 |
| Big Sioux River | 418 | 1,413 |
| Big Spring Creek | 14.4 | 14 |
| Black Dog Creek | 27.6 | 28 |
| Blackfoot Creek | 16.3 | 16 |
| Black Horse Butte Creek | 64.5 | 146 |
| Black Pipe Creek | 76.3 | 145 |
| Blacktail Creek | 30.3 | 80 |
| Blacktail Creek - North Fork | 12.3 | 12 |
| Blacktail Creek - South Branch | 20.1 | 20 |
| Blacktail Creek - South Fork | 17.4 | 17 |
| Blind Creek | 21.2 | 21 |
| Blood Run | 0 | 0 |
| Bloom Creek | 16.5 | 17 |
| Bois de Sioux River | 5.2 | 5 |
| Boxelder Creek (Cheyenne River tributary) | 137.8 | 152 |
| Boxelder Creek (Grand River - South Fork tributary) | 21.9 | 22 |
| Boxelder Creek (Little Missouri River tributary) | 9.9 | 10 |
| Box Spring Creek | 16.1 | 16 |
| Brave Bull Creek | 37 | 57 |
| Brave Bull Creek - West Fork | 19.6 | 20 |
| Bridger Creek | 49.4 | 49 |
| Brookfield Creek | 21.3 | 21 |
| Brule Creek | 41 | 81 |
| Brush Creek (Cheyenne River tributary) | 15.7 | 16 |
| Brush Creek (Grand River - South Fork tributary) | 14.7 | 15 |
| Brush Creek (Indian Creek (Hat Creek tributary)) | 1.4 | 1 |
| Brush Creek (Plum Creek (Bad River tributary)) | 22.6 | 23 |
| Brushy Creek | 48.2 | 86 |
| Buffalo Creek (Clarks Fork Creek tributary) | 22 | 22 |
| Buffalo Creek (Grand River - North Fork tributary) | 1.3 | 1 |
| Buffalo Creek (Keya Paha River tributary) | 9.9 | 10 |
| Buffalo Creek (Skunk Creek tributary) | 18.7 | 37 |
| Bull Creek (Belle Fourche River tributary) | 30.4 | 55 |
| Bull Creek (Cheyenne River tributary) | 16.9 | 17 |
| Bull Creek (Cheyenne River tributary) | 30.8 | 31 |
| Bull Creek (Cheyenne River tributary) | 30.8 | 31 |
| Bull Creek (Choteau Creek tributary) | 14 | 14 |
| Bull Creek (Frog Creek (Moreau River - South Fork tributary)) | 15.8 | 16 |
| Bull Creek (Grand River - South Fork tributary) | 45.3 | 45 |
| Bull Creek (Minnechaduza Creek tributary) | 14 | 14 |
| Bull Creek (Missouri River tributary) | 86.8 | 144 |
| Bull Creek - West Branch (Missouri River tributary) | 36.9 | 37 |
| Bull Creek (White River tributary) | 34 | 34 |
| Bullhead Run | 24.4 | 24 |
| Burnt Creek | 24.8 | 25 |
| Burnt Rock Creek | 14.3 | 14 |
| Butcher Creek (Grand River - South Fork tributary) | 21.2 | 21 |
| Butcher Creek (Red Scaffold Creek tributary) | 23.9 | 24 |
| Butte Creek | 41.1 | 41 |
| Buzzard Creek (Bad River tributary) | 37.9 | 38 |
| Buzzard Creek (Pass Creek tributary) | 33.3 | 59 |
| Cabin Creek | 19.1 | 19 |
| Cady Creek | 16 | 16 |
| Cain Creek (James River tributary) | 73.4 | 131 |
| Cain Creek (White River tributary) | 38.2 | 38 |
| Campbell Creek | 27.2 | 27 |
| Camp Creek (Sulphur Creek tributary) | 19.1 | 19 |
| Camp Creek (Vermillion River tributary) | 16.8 | 17 |
| Castle Creek | 45.1 | 45 |
| Cedar Bluff Creek | 18.6 | 19 |
| Cedar Boy Creek | 16.1 | 16 |
| Cedar Breaks Creek | 26.3 | 26 |
| Cedar Creek (Cheyenne River tributary) | 22.3 | 22 |
| Cedar Creek (Missouri River tributary) | 40 | 69 |
| Cedar Creek - South Branch (Missouri River tributary) | 14.5 | 15 |
| Cedar Creek - South Fork (Missouri River tributary) | 14.4 | 14 |
| Chantier Creek | 15.6 | 16 |
| Chapelle Creek | 52.8 | 92 |
| Charlie Creek | 26 | 26 |
| Cherry Creek | 125.4 | 1,074 |
| Cheyenne River | 320.8 | 6,213 |
| Choteau Creek | 105.4 | 119 |
| Clarks Fork Creek | 29.2 | 115 |
| Coal Bank Creek (Big Nasty Creek tributary) | 17.1 | 17 |
| Coal Bank Creek (Boxelder Creek (Little Missouri River tributary)) | 0.3 | 0 |
| Coal Creek | 28.2 | 28 |
| Cobb Creek | 36.5 | 37 |
| Coffee Creek (Little White River tributary) | 18.8 | 19 |
| Coffee Creek (Twelvemile Creek - South Fork tributary) | 18.9 | 19 |
| Cold Brook | 26.8 | 27 |
| Cold Springs Creek | 8 | 8 |
| Colton Creek | 20.5 | 21 |
| Cone Tree Creek | 20.9 | 21 |
| Corn Creek (Black Pipe Creek tributary) | 19 | 19 |
| Corn Creek (Turtle Creek (Bear-in-the-Lodge Creek tributary)) | 36.4 | 36 |
| Cottonwood Creek (Bad River - South Fork tributary) | 48.9 | 101 |
| Cottonwood Creek (Belle Fourche River tributary) | 15.3 | 15 |
| Cottonwood Creek (Black Pipe Creek tributary) | 15.6 | 16 |
| Cottonwood Creek (Black Pipe Creek tributary) | 17.1 | 17 |
| Cottonwood Creek (Cheyenne River tributary) | 36.4 | 36 |
| Cottonwood Creek (Cheyenne River tributary) | 45.3 | 86 |
| Cottonwood Creek (Cheyenne River tributary) | 53.9 | 54 |
| Cottonwood Creek (Grand River tributary) | 25.7 | 26 |
| Cottonwood Creek (Grand River tributary) | 24.8 | 25 |
| Cottonwood Creek (Keya Paha River tributary) | 7.2 | 7 |
| Cottonwood Creek (Moreau River - North Fork tributary) | 16.8 | 17 |
| Cottonwood Creek (Moreau River tributary) | 30.1 | 30 |
| Cottonwood Creek (Plum Creek (Bad River tributary)) | 18.6 | 19 |
| Cottonwood Creek (West Plum Creek tributary) | 16.6 | 17 |
| Cottonwood Creek (White River tributary) | 53.4 | 113 |
| Cottonwood Creek (White River tributary) | 28.2 | 45 |
| Cottonwood Creek (White River tributary) | 53 | 53 |
| Coyote Creek | 22.1 | 22 |
| Craven Creek | 29.5 | 30 |
| Crooked Creek (Cheyenne River tributary) | 16.2 | 35 |
| Crooked Creek (Grand River - North Fork tributary) | 39.6 | 40 |
| Crooked Creek (Plum Creek (Cheyenne River tributary)) | 16.3 | 16 |
| Crooked Creek - South Fork (Cheyenne River tributary) | 18.5 | 19 |
| Crooked Elm Creek | 16.1 | 16 |
| Crow Creek (Belle Fourche River tributary) | 26.6 | 27 |
| Crow Creek (Lost Creek (Lac qui Parle River - West Branch tributary)) | 14.3 | 14 |
| Crow Creek (Missouri River tributary) | 75.8 | 293 |
| Crow Creek (Redwater River tributary) | 12.4 | 30 |
| Crow Timber Creek | 15.3 | 15 |
| Cut Meat Creek | 53.6 | 84 |
| Darling Creek | 19.9 | 20 |
| Davis Creek | 14.4 | 14 |
| Dawson Creek | 38.2 | 38 |
| Deadman Creek | 14.4 | 14 |
| Deadmans Creek | 25.6 | 26 |
| De Bell Creek | 23.8 | 24 |
| Deep Bank Creek | 38.1 | 38 |
| Deep Creek (Cheyenne River tributary) | 29.7 | 30 |
| Deep Creek (Cheyenne River tributary) | 52.6 | 53 |
| Deep Creek (Moreau River tributary) | 61 | 101 |
| Deer Creek (Grand River tributary) | 19.8 | 20 |
| Deer Creek (Medary Creek tributary) | 36.6 | 37 |
| Deer Creek (Plum Creek (Cheyenne River tributary)) | 14.6 | 15 |
| Dirt Lodge Creek | 41.7 | 78 |
| Dirty Womans Creek | 15.5 | 16 |
| Dog Butte Creek | 20.3 | 20 |
| Dog Ear Creek | 76.1 | 130 |
| Double X Creek | 19.6 | 20 |
| Dove Creek | 40.7 | 41 |
| Dry Elm Creek | 15.6 | 16 |
| Dry House Creek | 14.9 | 15 |
| Dry Run (Firesteel Creek (James River tributary)) | 19.7 | 20 |
| Dry Run (James River tributary) | 59 | 59 |
| Dry Run (Willow Creek (Elm River (James River tributary))) | 23 | 23 |
| Duck Creek (Grand River - South Fork tributary) | 17.6 | 18 |
| Duck Creek (Hat Creek tributary) | 29.8 | 30 |
| Dupree Creek | 39.9 | 40 |
| Eagle Creek | 31.5 | 32 |
| Eagle Nest Creek | 38.1 | 38 |
| East Badlands Creek | 14.6 | 15 |
| East Brule Creek | 20.5 | 21 |
| East Cottonwood Creek | 14.5 | 15 |
| East Elm Creek | 51.8 | 52 |
| East Horse Creek | 22.1 | 22 |
| East Irish Creek | 14.1 | 14 |
| East Killdeer Creek | 27.4 | 27 |
| East Pearl Creek | 19.7 | 20 |
| East Tepee Creek | 10.5 | 11 |
| East Thunder Hawk Creek | 19.4 | 19 |
| East Twin Butte Creek - East Fork | 9.9 | 25 |
| East Twin Butte Creek - West Fork | 14.9 | 15 |
| East Union Creek | 15.4 | 15 |
| East White Horse Creek | 15.1 | 15 |
| Eightmile Creek | 35.7 | 36 |
| Elce Creek | 22.4 | 22 |
| Elk Creek | 148.4 | 267 |
| Elm Creek (Bear Creek (Moreau River tributary)) | 50.6 | 51 |
| Elm Creek (Belle Fourche River tributary) | 83.5 | 318 |
| Elm Creek (Crow Creek tributary) | 79.6 | 114 |
| Elm Creek (Sulphur Creek tributary) | 19.3 | 19 |
| Elm Creek - West Fork (Crow Creek tributary) | 34.5 | 35 |
| Elm Creek (Wolf Creek (James River tributary)) | 20.8 | 21 |
| Elm River (James River tributary) | 80.8 | 162 |
| Emanuel Creek | 67.3 | 88 |
| Enemy Creek | 55.4 | 55 |
| Fall River | 8 | 51 |
| False Bottom Creek | 34.9 | 35 |
| Felix Creek | 24.3 | 24 |
| Fifteen Creek | 20.3 | 20 |
| Firesteel Creek (Grand River tributary) | 69.9 | 85 |
| Firesteel Creek (James River tributary) | 93.7 | 168 |
| Firesteel Creek - West Branch (James River tributary) | 54.5 | 55 |
| Fisher Creek | 14.8 | 15 |
| Fishgut Creek | 23.2 | 44 |
| Fivemile Creek | 16.1 | 16 |
| Flandreau Creek | 12.8 | 13 |
| Flat Creek | 36.2 | 36 |
| Flint Creek | 26 | 26 |
| Flint Rock Creek | 58 | 75 |
| Flint Rock Creek - South Fork | 17.1 | 17 |
| Foot Creek | 71 | 71 |
| Fortyeight Mile Creek | 12.9 | 13 |
| Foster Creek | 68.9 | 69 |
| Fourmile Creek (Battle Creek (Moreau River - South Fork tributary)) | 33.9 | 34 |
| Fourmile Creek (Belle Fourche River tributary) | 31.2 | 31 |
| Fox Creek | 19.9 | 20 |
| French Creek | 92.7 | 116 |
| French Creek - South Fork | 23.5 | 24 |
| Frog Creek (Moreau River - South Fork tributary) | 25.3 | 41 |
| Frog Creek (Vermillion River tributary) | 17.6 | 18 |
| Frozen Horse Creek | 12.9 | 13 |
| Frozen Man Creek | 34.5 | 51 |
| Frozen Man Creek (Sulphur Creek tributary) | 22 | 40 |
| Gallup Creek | 21.2 | 21 |
| Gap Creek | 32.7 | 33 |
| Goose Creek (Moreau River - North Fork tributary) | 15.1 | 15 |
| Goose Creek (Moreau River tributary) | 19.5 | 20 |
| Grace Coolidge Creek | 27.8 | 28 |
| Grand River | 181.2 | 1,958 |
| Grand River - North Fork | 82.5 | 917 |
| Grand River - South Fork | 147.1 | 748 |
| Grass Creek | 29.9 | 30 |
| Gray Eagletail Creek | 13.9 | 14 |
| Green Grass Creek | 38.4 | 38 |
| Grindstone Creek | 36.8 | 37 |
| Grouse Creek | 23.2 | 23 |
| Handboy Creek | 22 | 22 |
| Hans Creek | 14.2 | 14 |
| Harding Creek | 19.6 | 20 |
| Hart Creek | 19.5 | 20 |
| Hat Creek | 45.4 | 147 |
| Hay Creek (Belle Fourche River tributary) | 32.8 | 33 |
| Hay Creek (Cedar Creek tributary) | 27.4 | 27 |
| Hay Creek (Moreau River - South Fork tributary) | 21.9 | 22 |
| Hay Creek (Moreau River - South Fork tributary) | 19.2 | 19 |
| Hay Creek (Redwater River tributary) | 23 | 23 |
| Herbert Creek | 37.5 | 38 |
| Herd Camp Creek | 27.8 | 28 |
| Hermaphrodite Creek | 47.4 | 62 |
| Hidewood Creek | 34.4 | 34 |
| High Bank Creek | 55.8 | 56 |
| Hilderbrand Creek | 18.8 | 19 |
| Hollow Creek | 29.6 | 30 |
| Holt Creek (Keya Paha River tributary) | 1.6 | 2 |
| Horse Creek (Belle Fourche River tributary) | 59.8 | 277 |
| Horse Creek (Grand River - North Fork tributary) | 27.3 | 27 |
| Horse Creek (Grand River - South Fork tributary) | 14.9 | 15 |
| Horse Creek (Little White River tributary) | 21.5 | 22 |
| Horse Creek (Sulphur Creek tributary) | 35 | 35 |
| Horse Creek (White River tributary) | 28.5 | 29 |
| Horsehead Creek | 77 | 112 |
| Hosupa Creek | 21.1 | 21 |
| Hot Brook | 15.9 | 16 |
| Howes Creek | 20 | 20 |
| Hump Creek | 44 | 44 |
| Hurley Creek | 20.4 | 20 |
| Indian Creek (Bad River tributary) | 37.7 | 61 |
| Indian Creek (Cheyenne River tributary) | 23.6 | 24 |
| Indian Creek (Hat Creek tributary) | 14.4 | 25 |
| Indian Creek (Horse Creek tributary) | 46.2 | 203 |
| Indian Creek (Rabbit Creek tributary) | 14.9 | 15 |
| Indian River | 17.1 | 17 |
| Irish Creek | 34.4 | 49 |
| Iron Creek | 17.6 | 18 |
| Iron Dog Creek | 32.5 | 33 |
| Isanti Creek | 21.8 | 22 |
| James River | 471.1 | 3,357 |
| Jim Creek | 50.5 | 51 |
| Joe Creek | 14.8 | 15 |
| Johnny Creek (Brushy Creek tributary) | 21.1 | 21 |
| Johnny Creek (White River tributary) | 20.5 | 21 |
| Johnson Creek | 20.8 | 21 |
| Jones Creek | 35.6 | 36 |
| Jorgenson River | 25.5 | 55 |
| Jug Creek | 17.4 | 17 |
| Kaiser Creek | 16.4 | 16 |
| Keya Paha River | 71.4 | 322 |
| Knife Creek | 14.5 | 15 |
| La Belle Creek | 15.7 | 16 |
| Lac qui Parle River | 1.8 | 117 |
| Lac qui Parle River - West Branch | 10.2 | 116 |
| Lake Creek (Cottonwood Creek (Bad River - South Fork tributary)) | 34.4 | 34 |
| Lake Creek (Little White River tributary) | 33.5 | 34 |
| Lame Johnny Creek | 34.8 | 35 |
| Lance Creek | 35.6 | 36 |
| Landing Creek | 23.6 | 24 |
| Larvie Creek | 16.8 | 17 |
| Lilly Creek | 13.9 | 14 |
| Limekiln Creek | 4.3 | 4 |
| Line Creek (Beaver Creek (Cheyenne River tributary)) | 4.8 | 5 |
| Line Creek (Thunder Butte Creek tributary) | 34.8 | 35 |
| Little Bear Creek | 24.3 | 24 |
| Little Cheyenne Creek | 30.9 | 31 |
| Little Cottonwood Creek (Cheyenne River tributary) | 38.4 | 38 |
| Little Cottonwood Creek (Cottonwood Creek (Cheyenne River tributary)) | 12 | 12 |
| Little Dog Creek | 16.7 | 17 |
| Little Emanuel Creek | 20.5 | 21 |
| Little Minnesota River | 66.4 | 121 |
| Little Missouri River | 76.2 | 230 |
| Little Moreau River | 48 | 48 |
| Little Nasty Creek | 19.2 | 19 |
| Little Oak Creek (Grand River tributary) | 19 | 19 |
| Little Oak Creek (Little White River tributary) | 16.8 | 17 |
| Little Prairie Dog Creek | 23.7 | 24 |
| Little Soldier Creek | 13.7 | 14 |
| Little Turtle Creek | 51.2 | 75 |
| Little Vermillion River | 47.2 | 47 |
| Little White River | 232.1 | 530 |
| Little Willow Creek | 15 | 15 |
| Little Wolf Creek | 23.8 | 24 |
| Lodgepole Creek | 47 | 47 |
| Lone Tree Creek (Bull Creek (Missouri River tributary)) | 20.3 | 20 |
| Lone Tree Creek (Cottonwood Creek (Bad River - South Fork tributary)) | 17.7 | 18 |
| Lone Tree Creek (Elk Creek tributary) | 13.8 | 14 |
| Lone Tree Creek (Grand River - North Fork tributary) | 7.5 | 8 |
| Lone Tree Creek (Hermaphrodite Creek tributary) | 14.1 | 14 |
| Lonetree Creek (Horse Creek (Belle Fourche River tributary)) | 14 | 14 |
| Lonetree Creek (James River tributary) | 20.5 | 49 |
| Lonetree Creek - South Branch (James River tributary) | 28.8 | 29 |
| Lonetree Creek (South Indian Creek tributary) | 13.3 | 13 |
| Lone Well Creek | 18 | 18 |
| Long Creek (Vermillion River tributary) | 56.1 | 95 |
| Long Creek (White River tributary) | 25.4 | 25 |
| Long Hollow Creek | 16.3 | 31 |
| Lost Creek (Keya Paha River tributary) | 10.1 | 10 |
| Lost Creek (Lac qui Parle River - West Branch tributary) | 18.3 | 48 |
| Lost Creek (Wolf Creek (Turtle Creek tributary)) | 46.9 | 47 |
| Lost Dog Creek | 19.6 | 20 |
| Louis Creek | 17.2 | 17 |
| Louse Creek | 16.4 | 16 |
| Luis Creek | 14.3 | 14 |
| Lute Creek | 12.4 | 12 |
| Madden Creek | 4.5 | 5 |
| Maple River (Elm River (James River tributary)) | 15.3 | 15 |
| Marne Creek | 22.8 | 23 |
| Masdon Creek | 22.8 | 23 |
| Matter Creek | 15.5 | 16 |
| Meadow Creek (Grand River tributary) | 17.2 | 17 |
| Meadow Creek (Moreau River tributary) | 35.3 | 35 |
| Meathook Creek | 15 | 15 |
| Medary Creek | 42 | 79 |
| Medicine Creek (Bad River tributary) | 37.2 | 37 |
| Medicine Creek (Missouri River tributary) | 127.4 | 250 |
| Medicine Creek - North Fork (Missouri River tributary) | 25.2 | 25 |
| Medicine Knoll Creek | 74.9 | 141 |
| Medicine Knoll Creek - South Fork | 66 | 66 |
| Medicine Root Creek | 51 | 126 |
| Mexican Creek | 34.5 | 35 |
| Middle Creek (Belle Fourche River tributary) | 20.6 | 21 |
| Middle Creek (Cherry Creek tributary) | 28.8 | 29 |
| Middle Creek (Grand River - South Fork tributary) | 14.8 | 15 |
| Middle Pearl Creek | 36 | 36 |
| Mill Iron Creek | 19.4 | 19 |
| Minnechaduza Creek | 18.1 | 32 |
| Minneconjou Creek | 13.4 | 46 |
| Minneconjou Creek - East Fork | 22.2 | 22 |
| Minneconjou Creek - West Fork | 10.5 | 11 |
| Minnesota River | 27.1 | 459 |
| Mission Creek | 23.4 | 23 |
| Missouri River | 505 | 24,533 |
| Mitchell Creek | 50.5 | 100 |
| Mixes Food Creek | 25.6 | 26 |
| Moccasin Creek | 42.8 | 114 |
| Monighan Creek | 21 | 21 |
| Moreau River | 290 | 2,262 |
| Moreau River - North Fork | 86.9 | 160 |
| Moreau River - South Fork | 135.8 | 472 |
| Morris Creek | 30 | 52 |
| Mosquito Creek | 16 | 16 |
| Moss Agate Creek | 13.5 | 22 |
| Moss Agate Creek - South Fork | 8.1 | 8 |
| Mud Creek (Bad River tributary) | 13.7 | 14 |
| Mud Creek (Big Sioux River tributary) | 24.8 | 25 |
| Mud Creek (Big Sioux River tributary) | 15.1 | 15 |
| Mud Creek (James River tributary) | 17 | 17 |
| Mud Creek (James River tributary) | 79.4 | 79 |
| Mud Creek (Red Scaffold Creek tributary) | 19 | 19 |
| Mud Creek (Yellow Bank River - South Fork tributary) | 21.5 | 22 |
| Mud Elm Creek | 21.3 | 21 |
| Mule Creek | 24.2 | 24 |
| Murphy Creek | 19.1 | 19 |
| Nail Creek | 23.9 | 24 |
| Narcelle Creek | 24.4 | 63 |
| Narcelle Creek - West Branch | 18.9 | 19 |
| Newton Fork | 14.7 | 15 |
| Ninemile Creek (Belle Fourche River tributary) | 27.3 | 27 |
| Ninemile Creek (Big Sioux River tributary) | 23 | 23 |
| No Flesh Creek | 33.2 | 33 |
| No Heart Creek | 23.7 | 24 |
| No Moccasin Creek | 39.1 | 39 |
| {no name} | 5.9 | 57 |
| North Buffalo Creek | 18.4 | 18 |
| North Cottonwood Creek | 16.4 | 16 |
| North Deer Creek | 48.9 | 94 |
| North Indian Creek | 39.6 | 91 |
| North Wolf Creek | 32.5 | 92 |
| Nowlin Creek | 16.3 | 16 |
| Oak Creek (Missouri River tributary) | 78.4 | 78 |
| Oak Creek (White River tributary) | 93.7 | 185 |
| Oat Creek | 9 | 9 |
| O'Donald Creek | 13.9 | 14 |
| Okobojo Creek | 80.3 | 80 |
| Owl Creek (Belle Fourche River tributary) | 79.7 | 80 |
| Owl Creek (Dog Ear Creek tributary) | 24.3 | 24 |
| Palmer Creek | 15.4 | 15 |
| Paradis Creek | 24.6 | 25 |
| Pass Creek (Beaver Creek (Cheyenne River tributary)) | 20.1 | 20 |
| Pass Creek (White River tributary) | 70.1 | 129 |
| Pattee Creek | 18.3 | 18 |
| Patterson Creek | 13.9 | 14 |
| Pearl Creek (Cain Creek (James River tributary)) | 21.7 | 57 |
| Pearl Creek (James River tributary) | 72 | 169 |
| Pearl Creek - South Fork (James River tributary) | 61.1 | 61 |
| Pease Creek | 30.3 | 30 |
| Peck Creek | 19.7 | 20 |
| Peggy Creek | 25.4 | 25 |
| Peg Munky Run | 17.8 | 18 |
| Phister Creek | 16.7 | 17 |
| Pierre Creek | 23.2 | 23 |
| Pine Creek (Cheyenne River tributary) | 21.5 | 22 |
| Pine Creek (Little White River tributary) | 18.2 | 64 |
| Pine Creek - North Branch (Little White River tributary) | 22.5 | 23 |
| Pine Creek - South Branch (Little White River tributary) | 23 | 23 |
| Pine Creek (Sulphur Creek tributary) | 34.7 | 35 |
| Pine Spring Creek | 14.3 | 14 |
| Pipestone Creek | 31.8 | 32 |
| Pitan Creek | 14.6 | 15 |
| Platte Creek | 58.9 | 77 |
| Platte Creek - East Fork | 17.7 | 18 |
| Pleasant Valley Creek | 22.4 | 22 |
| Plum Creek (Bad River tributary) | 63.3 | 161 |
| Plum Creek (Cedar Creek tributary) | 1.3 | 1 |
| Plum Creek (Cheyenne River tributary) | 60 | 197 |
| Plum Creek (Cheyenne River tributary) | 14.3 | 14 |
| Plum Creek (Grand River tributary) | 17.2 | 17 |
| Plum Creek (James River tributary) | 26.1 | 26 |
| Plum Creek (Little Missouri River tributary) | 8.4 | 8 |
| Poeno Creek | 14.4 | 14 |
| Ponca Creek | 93.2 | 135 |
| Pony Creek | 31.1 | 31 |
| Pooley Creek | 23.3 | 23 |
| Porcupine Creek (Black Pipe Creek tributary) | 17.3 | 17 |
| Porcupine Creek (North Indian Creek tributary) | 20.4 | 20 |
| Porcupine Creek (White River tributary) | 75.6 | 76 |
| Potato Creek | 48.7 | 49 |
| Prairie Creek | 19.8 | 20 |
| Pretty Creek | 15 | 15 |
| Rabbit Creek | 130.3 | 275 |
| Randall Creek | 16.8 | 17 |
| Rapid Creek | 128.5 | 222 |
| Rattlesnake Creek | 57.8 | 58 |
| Red Butte Creek | 14.4 | 14 |
| Red Coat Creek | 37.8 | 38 |
| Red Earth Creek | 51 | 51 |
| Red Owl Creek | 67.2 | 110 |
| Red Scaffold Creek | 55.8 | 114 |
| Red Shirt Creek | 17.7 | 18 |
| Redstone Creek | 112.7 | 154 |
| Red Stone Creek | 33.2 | 33 |
| Redwater Creek (Moreau River tributary) | 31.6 | 32 |
| Redwater Creek (Redwater River tributary) | 6.8 | 15 |
| Redwater Creek (White River tributary) | 38.9 | 39 |
| Redwater River | 32.7 | 182 |
| Red Willow Creek | 22.7 | 23 |
| Ree Creek | 43.2 | 43 |
| Rieger Creek | 23.7 | 24 |
| Rock Creek (Grand River tributary) | 35.1 | 35 |
| Rock Creek (James River tributary) | 107.1 | 130 |
| Rock Creek (Keya Paha River tributary) | 38 | 38 |
| Roundup Creek | 14.7 | 15 |
| Rousseau Creek | 3.8 | 41 |
| Rousseau Creek - East Branch | 16 | 16 |
| Rousseau Creek - West Branch | 21.4 | 21 |
| Rudy Creek | 41.5 | 108 |
| Rudy Creek - East Fork | 26.5 | 27 |
| Runs Close Creek | 15.9 | 16 |
| Rush Creek | 17 | 17 |
| Saddle Creek | 23.7 | 39 |
| Sage Creek | 41.6 | 73 |
| Sage Creek - Middle Fork | 13.8 | 14 |
| Sage Creek - South Fork | 17.9 | 18 |
| Sand Creek (Cheyenne River tributary) | 22.1 | 22 |
| Sand Creek (James River tributary) | 97.3 | 123 |
| Sand Creek (Keya Paha River tributary) | 44.2 | 44 |
| Sand Creek (Moreau River - South Fork tributary) | 45.2 | 45 |
| Sand Creek (Thunder Creek tributary) | 26.8 | 27 |
| Sansarc Creek | 41.7 | 65 |
| Sansarc Creek - North Fork | 23.6 | 24 |
| Sarah Laribee Creek | 16 | 16 |
| Scabby Creek | 15.3 | 15 |
| Sedlano Creek | 20.1 | 20 |
| Settin Up Creek | 25.3 | 25 |
| Shadley Creek | 16.7 | 17 |
| Shaefer Creek | 43.9 | 59 |
| Shaw Creek | 16.2 | 16 |
| Sheep Creek (Grand River - South Fork tributary) | 19.2 | 19 |
| Sheep Creek (Moreau River - North Fork tributary) | 24.9 | 25 |
| Shortfoot Creek | 19.9 | 20 |
| Shue Creek | 46.5 | 47 |
| Silver Creek | 25.5 | 26 |
| Sioux Creek | 16.7 | 17 |
| Sixmile Creek | 44.7 | 45 |
| Skull Creek | 18.5 | 19 |
| Skunk Creek | 63.2 | 174 |
| Skunk Creek - West Branch | 23.7 | 24 |
| Slate Creek | 28.8 | 29 |
| Slaughter Creek | 17.6 | 34 |
| Slim Butte Creek | 47.7 | 48 |
| Slim Buttes Creek | 12.9 | 48 |
| Slip-up Creek | 25.7 | 26 |
| Smith Creek | 87.5 | 103 |
| Smith Creek - East Fork | 15.6 | 16 |
| Snake Creek (Grand River - South Fork tributary) | 16.7 | 17 |
| Snake Creek (Grand River tributary) | 35.3 | 35 |
| Snake Creek (James River tributary) | 118.1 | 337 |
| Snake Creek (Missouri River tributary) | 21.5 | 22 |
| Snake Creek - North Fork (James River tributary) | 54.6 | 55 |
| Snake Creek (Saddle Creek tributary) | 15.2 | 15 |
| Snake Creek - South Fork (James River tributary) | 123.8 | 219 |
| Snatch Creek | 33.2 | 33 |
| Soft Water Creek | 22.9 | 45 |
| Soldier Creek (Inyan Kara Creek tributary) | 1.6 | 2 |
| Soldier Creek (Missouri River tributary) | 17 | 17 |
| South Chapelle Creek | 39.5 | 40 |
| South Creek (Bad River tributary) | 24.1 | 24 |
| South Creek (Indian Creek (Bad River tributary)) | 23.5 | 24 |
| South Creek (West Plum Creek tributary) | 13.8 | 14 |
| South Indian Creek | 33.5 | 47 |
| South Long Hollow Creek | 14.6 | 15 |
| South Sulphur Creek | 31.4 | 31 |
| South Willow Creek | 14 | 14 |
| Spearfish Creek | 46.5 | 47 |
| Split Rock Creek | 27.6 | 120 |
| Spook Creek | 14.8 | 15 |
| Spotted Bear Creek | 3.2 | 33 |
| Spotted Bear Creek - East Fork | 17 | 17 |
| Spotted Bear Creek - West Fork | 12.8 | 13 |
| Spring Creek (Bear Butte Creek tributary) | 34.9 | 35 |
| Spring Creek (Bear-in-the-Lodge Creek tributary) | 23.7 | 24 |
| Spring Creek (Big Sioux River tributary) | 25.6 | 26 |
| Spring Creek (Cheyenne River tributary) | 148.1 | 163 |
| Spring Creek (Frozen Man Creek (Sulphur Creek tributary)) | 17.5 | 18 |
| Spring Creek (Missouri River tributary) | 103.2 | 103 |
| Spring Creek (Moreau River - North Fork tributary) | 16.5 | 17 |
| Spring Creek (White River tributary) | 22.6 | 23 |
| Spur Creek | 19.3 | 19 |
| Standing Cloud Creek | 15.2 | 15 |
| Station Elm Creek | 25.3 | 25 |
| Stink Creek | 40.2 | 73 |
| Stinkingwater Creek | 24.4 | 24 |
| Stinking Water Creek | 24 | 24 |
| Stockade Beaver Creek | 1.2 | 1 |
| Stony Butte Creek (Brushy Creek tributary) | 17.1 | 17 |
| Stony Butte Creek (Medicine Creek (Missouri River tributary)) | 35.6 | 36 |
| Stony Run | 17.1 | 17 |
| Straighthead Creek | 20 | 20 |
| Stray Horse Creek | 29 | 29 |
| Sully Creek | 15.7 | 16 |
| Sulphur Creek | 126 | 305 |
| Swan Creek (Missouri River tributary) | 40.1 | 64 |
| Swan Creek (Moreau River tributary) | 21.6 | 22 |
| Tahc’a Okute Wakpa | 24.7 | 25 |
| Tahc’a Okute Wakpa C’ikala | 15.8 | 16 |
| Tall Prairie Chicken Creek | 15.5 | 16 |
| Tepee Creek | 7.8 | 33 |
| Thunder Butte Creek | 145.5 | 253 |
| Thunder Creek | 72.3 | 99 |
| Thunder Hawk Creek | 32 | 51 |
| Tie Creek (Little Missouri River tributary) | 1 | 1 |
| Timber Creek (Antelope Creek (Missouri River tributary)) | 13.8 | 14 |
| Timber Creek (Cheyenne River tributary) | 32.2 | 32 |
| Timber Creek (James River tributary) | 50.2 | 50 |
| Trail Creek | 25.6 | 26 |
| Turkey Ridge Creek | 52.9 | 53 |
| Turtle Creek (Bear-in-the-Lodge Creek tributary) | 14 | 50 |
| Turtle Creek (Cherry Creek tributary) | 17.7 | 18 |
| Turtle Creek (James River tributary) | 125.3 | 476 |
| Twelvemile Creek | 52.3 | 145 |
| Twelvemile Creek - South Fork | 42.3 | 61 |
| Twin Butte Creek | 21.1 | 46 |
| Two Nation Creek | 24.4 | 24 |
| Union Creek | 1.7 | 29 |
| Valley Creek | 38.7 | 39 |
| Veo Creek | 15.9 | 16 |
| Vermillion River | 96.1 | 627 |
| Vermillion River - East Fork | 98.5 | 146 |
| Vermillion River - West Fork | 108.1 | 108 |
| Virgin Creek | 57.7 | 58 |
| Wagonhound Creek | 16.4 | 16 |
| War Creek | 8.5 | 52 |
| War Creek - East Branch | 22.1 | 22 |
| War Creek - West Branch | 21.6 | 22 |
| Waterhole Creek | 23.3 | 23 |
| West Badlands Creek | 15.3 | 15 |
| West Brule Creek | 19.3 | 19 |
| West Bull Creek | 24.9 | 25 |
| West Cottonwood Creek | 21.1 | 21 |
| West Elm Creek | 23.2 | 122 |
| West Horse Creek | 22.8 | 23 |
| West Pearl Creek | 15.9 | 16 |
| West Pipestone Creek | 43.4 | 43 |
| West Plum Creek | 75.3 | 106 |
| West Redstone Creek | 41.2 | 41 |
| West Tepee Creek | 14.6 | 15 |
| West Union Creek | 12.3 | 12 |
| Whetstone Creek | 5.6 | 112 |
| Whetstone Creek - North Fork | 40.2 | 40 |
| Whetstone Creek - South Fork | 51.6 | 52 |
| Whetstone River | 12.7 | 92 |
| Whetstone River - North Fork | 42.5 | 43 |
| Whetstone River - South Fork | 37.1 | 37 |
| White Clay Creek (Bad River tributary) | 37.5 | 72 |
| White Clay Creek - East Branch (Bad River tributary) | 34.6 | 35 |
| White Clay Creek (White River tributary) | 42 | 65 |
| White Hill Creek | 20.2 | 20 |
| Whitehorse Creek | 21.7 | 42 |
| White Horse Creek (Oak Creek (White River tributary)) | 11.4 | 27 |
| White Horse Creek (Wounded Knee Creek tributary) | 16.3 | 16 |
| White Owl Creek | 42.3 | 42 |
| White River | 441.8 | 3,532 |
| White Shirt Creek | 27.5 | 28 |
| White Thunder Creek | 61.8 | 62 |
| Whitewater Creek | 40.1 | 40 |
| White Willow Creek | 35.1 | 35 |
| Whitewood Creek | 47 | 47 |
| Wilburn Creek | 20.8 | 21 |
| Wild Rice Creek | 20.1 | 20 |
| Williams Creek | 23 | 23 |
| Willow Creek (Bad River tributary) | 51.4 | 51 |
| Willow Creek (Belle Fourche River tributary) | 53 | 84 |
| Willow Creek (Big Sioux River tributary) | 33.1 | 33 |
| Willow Creek - East Branch (Missouri River tributary) | 24.8 | 25 |
| Willow Creek (Elm River (James River tributary)) | 42.4 | 65 |
| Willow Creek (Grand River tributary) | 34.6 | 35 |
| Willow Creek (Keya Paha River tributary) | 27.7 | 28 |
| Willow Creek (Skunk Creek tributary) | 29.1 | 29 |
| Willow Creek - West Branch (Missouri River tributary) | 21.6 | 22 |
| Willow Creek - West Fork (White River tributary) | 16 | 16 |
| Willow Creek (White River tributary) | 9.8 | 26 |
| Wilson Creek (Grand River - North Fork tributary) | 11 | 11 |
| Wind Creek | 27.4 | 27 |
| Witcher Holes Creek | 28.8 | 29 |
| Wolf Creek - East Prong (White Clay Creek (White River tributary)) | 11 | 11 |
| Wolf Creek (James River tributary) | 70 | 91 |
| Wolf Creek (Missouri River tributary) | 27 | 27 |
| Wolf Creek - South Prong (White Clay Creek (White River tributary)) | 7 | 7 |
| Wolf Creek (Turtle Creek tributary) | 93.6 | 232 |
| Wolf Creek (White Clay Creek (White River tributary)) | 4.9 | 23 |
| Wounded Knee Creek | 84.2 | 101 |
| Yellow Bank River - North Fork | 49.2 | 49 |
| Yellow Bank River - South Fork | 30.4 | 52 |
| Yukmi Creek | 18.4 | 18 |
