| Cottonwood Lake (SRA) | NE | Lake | Not Supporting | 2 | 44 |
| Cozad Lake (WMA) | NE | Lake | Not Supporting | 1 | 17 |
| Crescent Lake | NE | Lake | Not Supporting | 2 | 1,007 |
| Crystal Cove Lake (South Sioux City) | NE | Lake | Fully Supporting | 0 | 32 |
| Crystal Lake | NE | Lake | Not Supporting | 1 | 6.00 |
| Crystal Lake (SRA) | NE | Lake | Not Supporting | 5 | 5.00 |
| Crystal Springs Center Lake | NE | Lake | Not Supporting | 4 | 6.00 |
| Crystal Springs East Lake | NE | Lake, Freshwater | Not Supporting | 4 | 8.27 |
| Crystal Springs Northwest Lake | NE | Lake | Not Supporting | 4 | 6.00 |
| Cub Creek Lake | NE | Lake | Not Supporting | 4 | 36 |
| Cub Creek Lake | NE | Lake | Not Supporting | 2 | 31 |
| Curtis City Pond | NE | Lake, Freshwater | Not Supporting | 2 | 1.00 |
| Czechland Lake | NE | Lake | Not Supporting | 5 | 69 |
| David City Park Lake | NE | Lake | Not Supporting | 3 | 5.00 |
| Davis Creek Reservoir | NE | Lake | Not Supporting | 1 | 978 |
| Diamond Lake South | NE | Lake | Not Supporting | 5 | 20 |
| Donald Whitney Memorial Lake | NE | Lake, Freshwater | Not Supporting | 4 | 13 |
| Duck Creek Lake | NE | Lake | Not Supporting | 1 | 54 |
| East Hershey Lake (WMA) | NE | Lake | Not Supporting | 1 | 28 |
| East Mormon Island Lake (SRA) | NE | Lake | Not Supporting | 1 | 19 |
| East Odessa Lake (WMA) | NE | Lake | Not Supporting | 1 | 7.00 |
| East Sutherland Lake (WMA) | NE | Lake | Not Supporting | 1 | 28 |
| East Twin Lake | NE | Lake | Not Supporting | 4 | 149 |
| Ed Zorinsky Lake (site No. 18) | NE | Lake | Not Supporting | 3 | 235 |
| Elwood Reservoir | NE | Lake, Freshwater | Not Supporting | 1 | 978 |
| Enders Reservoir | NE | Lake | Not Supporting | 2 | 1,194 |
| Falls City Lake (Stanton Lake) | NE | Lake | Fully Supporting | 0 | 4.00 |
| Fremont Lake No. 1 (SRA) | NE | Lake | Not Supporting | 5 | 14 |
| Fremont Lake No. 10 (SRA) | NE | Lake | Not Supporting | 3 | 40 |
| Fremont Lake No. 11 (SRA) | NE | Lake, Freshwater | Not Supporting | 1 | 6.50 |
| Fremont Lake No. 12 (SRA) | NE | Lake | Not Supporting | 3 | 7.00 |
| Fremont Lake No. 15 (Victory) (SRA) | NE | Lake | Not Supporting | 3 | 55 |
| Fremont Lake No. 16 (SRA) | NE | Lake | Not Supporting | 3 | 13 |
| Fremont Lake No. 17 (Sra) | NE | Lake, Freshwater | Not Supporting | 4 | 5.52 |
| Fremont Lake No. 18E (SRA) | NE | Lake | Not Supporting | 1 | 10 |
| Fremont Lake No. 19 (SRA) | NE | Lake | Not Supporting | 1 | 3.00 |
| Fremont Lake No. 2 (SRA) | NE | Lake | Not Supporting | 2 | 18 |
| Fremont Lake No. 20 (SRA) | NE | Lake | Not Supporting | 4 | 46 |
| Fremont Lake No. 3 (Sra) | NE | Lake, Freshwater | Not Supporting | 4 | 3.29 |
| Fremont Lake No. 4 (SRA) | NE | Lake | Not Supporting | 4 | 6.00 |
| Fremont Lake No. 5 (Sra) | NE | Lake, Freshwater | Not Supporting | 4 | 13 |
| Fremont Lake No. 7 and 8 (SRA) | NE | Lake | Not Supporting | 4 | 12 |
| Fremont Lake No. 9 (SRA) | NE | Lake | Not Supporting | 3 | 12 |
| Frenchman East Lake (WMA) | NE | Lake | Not Supporting | 1 | 5.00 |
| Frenchman Middle Lake (WMA) | NE | Lake | Not Supporting | 1 | 6.00 |
| Frenchman West Lake (WMA) | NE | Lake | Not Supporting | 1 | 9.00 |
| Frye Lake | NE | Lake, Freshwater | Not Supporting | 1 | 255 |
| Ft. Kearny Lake No. 2 | NE | Lake, Freshwater | Fully Supporting | 0 | 3.00 |
| Ft. Kearny Lake No. 3 | NE | Lake, Freshwater | Fully Supporting | 0 | 3.00 |
| Ft. Kearny Lake No. 4 | NE | Lake, Freshwater | Fully Supporting | 0 | 3.00 |