North East
Rio Grande
Pecos Wilderness Area
- Pecos River
- Rio Mora
- Jack’s Creek
- Pancuela Creek
- Horsethief
- Windsor Creek
- Alpine Lake
- Baldy Lake
- Katherine Lake
- Stewart Lake
Taos Area
- Rio Pueblo de Taos
- Rio Chiquito
- Rito de la Olla
- Rio Hondo
- Embudo Creek
- Rio Pueblo
Red River Area
- Red River
- Cabresto Lake
- Middle Fork Lake
- Cimarron River
- Coyote Creek
- Eagle Nest Lake
- Valle Vidal
- Costilla Creek
- Comanche Creek
- Shuree Ponds
- Latir Lakes
Santa Fe Area
- Rio Santa Cruz
- Rio del Medio
- Rio Frijoles