| Apache Box |
| Big Hatchet Mountains |
| Black Range Mountains |
| Bootheel |
| Conchas Reservoir |
| Eagle Nest Lake |
| Guadalupe Mountains |
| Jemez Mountains |
| Lower Gila River |
| Lower Pecos and Black Rivers |
| Lower Rio Grande |
| Lower Rio Grande - Caballo Reservoir |
| Middle Pecos River |
| Middle Rio Grande |
| Middle San Juan River |
| Mimbres River |
| Northern Sacramento and Capitan Mountains |
| Organ Mountains |
| Pecos River - Lake Sumner |
| Pecos River Headwaters |
| Rio Chama |
| Rio Puerco |
| San Francisco River |
| San Mateo Mountains |
| Santa Fe River |
| Southern Sacramento Mountains |
| Upper Gila River |
| Upper Rio Grande |
| Upper San Juan River |
| Vermejo River |