| Skyview Lake | NE | Lake | Not Supporting | 1 | 39 |
| Smith Lake (Crescent Lake NWR) | NE | Lake | Not Supporting | 1 | 39 |
| Smith Lake (WMA) | NE | Lake | Not Supporting | 1 | 219 |
| South Morrill Sandpit | NE | Lake | Not Supporting | 1 | 5.00 |
| Stagecoach Lake | NE | Lake | Not Supporting | 6 | 171 |
| Standing Bear Lake (Site No. 16) | NE | Lake | Not Supporting | 5 | 105 |
| Steinhart Park Lake (Nebraska City) | NE | Lake | Not Supporting | 1 | 1.00 |
| Summit Lake | NE | Lake | Not Supporting | 3 | 180 |
| Sutherland Cooling Pond | NE | Lake/Reservoir/Pond | Not Supporting | 1 | Filed as 0 |
| Sutherland Reservoir | NE | Lake | Fully Supporting | 0 | 2,954 |
| Swan Creek Lake (2A) | NE | Lake | Not Supporting | 1 | 30 |
| Swan Creek Lake (5A) | NE | Lake | Not Supporting | 5 | 87 |
| Swanson Reservoir | NE | Lake | Not Supporting | 3 | 4,660 |
| Swanton Lake | NE | Lake | Not Supporting | 4 | 23 |
| Timber Point Lake (6C) | NE | Lake | Not Supporting | 1 | 22 |
| Tree Claim Lake (Crescent Lake NWR) | NE | Lake, Freshwater | Not Supporting | 1 | 6.00 |
| Twin Lake R.C. - North Lake (WMA) | NE | Lake | Not Supporting | 1 | 118 |
| Twin Lake R.C. - South Lake (WMA) | NE | Lake | Not Supporting | 1 | 82 |
| Two Rivers Lake No. 1 and 2 (SRA) | NE | Lake, Freshwater | Not Supporting | 1 | 8.30 |
| Union Pacific Lake (Sra) | NE | Lake, Freshwater | Not Supporting | 1 | 15 |
| Valentine Mill Pond | NE | Lake | Not Supporting | 4 | 16 |
| Verdon Lake (SRA) | NE | Lake | Not Supporting | 1 | 30 |
| Wagon Train Lake | NE | Lake | Not Supporting | 5 | 298 |
| Walgren Lake (Sra) | NE | Lake, Freshwater | Not Supporting | 1 | 108 |
| Walnut Creek Lake | NE | Lake | Not Supporting | 4 | 83 |
| Walnut Creek Lake (2A) | NE | Lake | Not Supporting | 4 | 18 |
| War Axe (Sra) | NE | Lake, Freshwater | Not Supporting | 1 | 16 |
| Weeping Water City Lake | NE | Lake | Fully Supporting | 0 | 4.00 |
| Wehrspann Lake (Site No. 20) | NE | Lake | Not Supporting | 5 | 215 |
| Wellfleet Lake | NE | Lake | Not Supporting | 1 | 46 |
| West Brady Lake (WMA) | NE | Lake | Not Supporting | 1 | 7.00 |
| West Gothenburg Lake (WMA) | NE | Lake, Freshwater | Fully Supporting | 0 | 15 |
| West Long Lake (Valentine NWR) | NE | Lake, Freshwater | Not Supporting | 1 | 74 |
| West Mormon Island Lake (SRA) | NE | Lake | Not Supporting | 1 | 44 |
| West Point City Lake (Neligh Park Lake) | NE | Lake | Not Supporting | 4 | 3.00 |
| West Twin Lake | NE | Lake, Freshwater | Not Supporting | 4 | 45 |
| Whitney Reservoir | NE | Lake | Not Supporting | 1 | 962 |
| Wild Plum Lake (26A) | NE | Lake | Not Supporting | 1 | 13 |
| Wildwood Lake | NE | Lake | Not Supporting | 5 | 109 |
| Willow Creek Reservoir | NE | Lake | Not Supporting | 5 | 769 |
| Wilson Creek Lake 2X (WMA) | NE | Lake | Not Supporting | 1 | 15 |
| Windmill Lake No. 1 (SRA) | NE | Lake | Not Supporting | 1 | 9.00 |
| Windmill Lake No. 2 (SRA) | NE | Lake, Freshwater | Fully Supporting | 0 | 1.50 |
| Windmill Lake No. 3 (SRA) | NE | Lake, Freshwater | Fully Supporting | 0 | 2.00 |
| Windmill Lake No. 4 (SRA) | NE | Lake, Freshwater | Fully Supporting | 0 | 4.00 |
| Windmill Lake No. 5 (SRA) | NE | Lake | Fully Supporting | 0 | 7.00 |
| Windmill Lake No. 6 (SRA) | NE | Lake, Freshwater | Fully Supporting | 0 | 2.00 |
| Wirth Brothers Lake (Site 27) | NE | Lake | Not Supporting | 1 | 26 |
| Wolf Wildcat Lake | NE | Lake | Not Supporting | 1 | 40 |
| Yankee Hill Lake | NE | Lake | Not Supporting | 5 | 183 |