| Watershed and Affected Areas by Agriculture or Related | Propable Cause Related to Agriculture |
| Canadian Headwaters: | |
| Chicorica Creek (Canadain River to Raton Creek) | Rangeland Grazing |
| Raton Creek (Chicorica Creek to Headwaters) | Rangeland Grazing |
| VanBremmer Creek(hwy 64 TO Headwaters) | Rangeland Grazing |
| Vermejo River (Rail Canyon to York Canyon) | Rangeland Grazing |
| Vermejo River (York Canyon to headwaters) | Rangeland Grazing |
| Cimarron: | |
| Cieneguilla Creek (Eagle Nest Lake to headwaters) | Rangeland Grazing |
| Eagle Nest Lake | Rangeland Grazing |
| Middle Ponil Creek (South Ponil to headwaters) | Rangeland Grazing |
| Moreno Creek (Eagle Nest Lake to headwaters) | Rangeland Grazing |
| North Ponil Creek (South Ponil Creek to McCrystal Creek) | Rangeland Grazing |
| Ponil Creek (Cimarron River to US 64) | Rangeland Grazing |
| Ponil Creek (US 64 to confl of North & South Ponil) | Rangeland Grazing |
| Rayado Creek (Cimarron River to Miami Lake Diversion) | Rangeland Grazing |
| Sixmile Creek (Eagle Nest Lake to headwaters) | Rangeland Grazing, Animal Feeding Operations (NPS), Livestock (Grazing or Feeding Operations) |
| Upper Canadian: | |
| Conchas Reservoir | Rangeland Grazing |
| Mora: | |
| Coyote Creek (Mora River to Black Lake) | Rangeland Grazing |
| Little Coyote Creek (Black Lake to headwaters) | Rangeland Grazing |
| Mora River (HWY 434 to headwaters) | Rangeland Grazing |
| Morphy (Murphy) Lake | Rangeland Grazing |
| Conejos: | |
| Rio de los Pinos (New Mexico reaches) | Rangeland Grazing |
| Upper Rio Grande: | |
| Comanche Creek (Costilla Creek to headwaters) | Rangeland Grazing |
| Costilla Creek (Diversion abv Costilla to Comanche Creek) | Rangeland Grazing |
| Embudo Creek (Rio Grande to Canada de Ojo Sarco) | Rangeland Grazing |
| Goose Lake | Rangeland Grazing |
| Rio Fernando de Taos (Rio Pueblo de Taos to Tienditas Creek) | Rangeland Grazing |
| Rio Grande (non-pueblo Santa Clara to Embudo Creek) | Rangeland Grazing and Irrigated Crop Production |
| Rio Hondo (Rio Grande to USFS bnd) | Rangeland Grazing |
| Rio Pueblo (Picuris Pueblo bnd to headwaters) | Rangeland Grazing |
| Rio Pueblo de Taos (Arroyo del Alamo to R Grande del Rancho) | Rangeland Grasing and Crop Production (Crop land or dry land) |
| Rio Pueblo de Taos (R Grande del Rancho to Taos pueblo bnd) | Rangeland Grazing |
| Rio Pueblo de Taos (Rio Grande to Arroyo del Alamo) | Rangeland Grazing |
| Rio Santa Barbara (Picuris Pueblo bnd to USFS bnd) | Rangeland Grazing |
| Santa Cruz River (San Clara Pueblo bnd to Santa Cruz Dam) | Irrigated Crop Production |
| Rio Chama: | |
| Abiquiu Creek (Rio Chama to headwaters) | Rangeland Grazing |
| Canjilon Ck (Perennial portions Abiquiu Rsrv to headwaters) | Agriculture |
| Cañones Creek (Abiquiu Reservoir to headwaters) | Rangeland Grazing |
| Cecilia Canyon Creek (Rio Capulin to USFS bnd) | Rangeland Grazing |
| Clear Creek (Rio Gallina to headwaters) | Rangeland Grazing |
| Hopewell Lake | Rangeland Grazing |
| Poleo Creek (Rio Puerco de Chama to headwaters) | Rangeland Grazing |
| Polvadera Creek (Cañones Creek to headwaters) | Rangeland Grazing |
| Rio Chama (Rio Brazos to Little Willow Creek) | Rangeland Grazing |
| Rio Chamita (Rio Chama to CO border) | Rangeland Grazing |
| Rio Nutrias (Rio Chama to headwaters) | Rangeland Grazing and Crop Production (Crop Land or Dry Land) |
| Rio Puerco de Chama (Abiquiu Reservoir to Poleo Creek) | Rangeland Grazing |
| Rio Tusas (Rio Vallecitos to headwaters) | Rangeland Grazing |
| Rio Vallecitos (Rio Tusas to headwaters) | Rangeland Grazing and Irrigated Crop Production |
| Rito de Tierra Amarilla (Rio Chama to HWY 64) | Rangeland Grazing |
| Rito Resumidero (Rio Puerco de Chama to Headwaters) | Rangeland Grazing |
| Rio Grande-Santa Fe: | |
| Galisteo Ck (Intermittent reaches abv Santo Domingo bnd) | Rangeland Grazing |
| Santa Fe River (Cochiti Pueblo bnd to Santa Fe WWTP) | Rangeland Grazing |
| Jemez: | |
| East Fork Jemez (San Antonio Creek to VCNP bnd) | Rangeland Grazing |
| East Fork Jemez (VCNP to headwaters) | Rangeland Grazing |
| Fenton Lake | Rangeland Grazing |
| Jaramillo Creek (East Fork Jemez to headwaters) | Rangeland Grazing |
| Jemez River (Rio Guadalupe to Soda Dam nr Jemez Springs) | Rangeland Grazing |
| Jemez River (Soda Dam nr Jemez Springs to East Fork) | Rangeland Grazing |
| Redondo Creek ( VCNP bnd to headwaters ) | Rangeland Grazing |
| Redondo Creek (Sulphur Creek to VCNP) | Rangeland Grazing |
| Rio Cebolla (Fenton Lake to headwaters) | Rangeland Grazing |
| Rio Cebolla (Rio de las Vacas to Fenton Lake) | Rangeland Grazing |
| Rio de las Vacas (Rio Cebolla to Clear Creek) | Rangeland Grazing |
| Rio Guadalupe (Jemez River to confl with Rio Cebolla) | Rangeland Grazing |
| Rito Peñas Negras (Rio de las Vacas to headwaters) | Rangeland Grazing |
| San Antonio Creek (East Fork Jemez to VCNP bnd) | Rangeland Grazing |
| San Antonio Creek (VCNP bnd to headwaters) | Rangeland Grazing |
| Rio Puerco: | |
| Rio Puerco (Arroyo Chijuilla to northern bnd Cuba) | Rangeland Grazing |
| Rio San Jose: | |
| Bluewater Creek (Bluewater Rsrv to headwaters) | Rangeland Grazing |
| Bluewater Creek (non-tribal Rio San Jose to Bluewater Rsvr) | Rangeland Grazing |
| Rio Moquino (Laguna Pueblo to Seboyettia Creek) | Rangeland Grazing |
| El Paso/Las Cruces: | |
| Rio Grande(Anthony Bridge to Picacho Bridge) | Rangeland Grazing, Permitted Runoff from Confined Animal Feeding Operations (CAFOs) |
| Rio Grande (International Mexico bnd to Anthony Bridge) | Rangeland Grazing, Permitted Runoff from Confined Animal Feeding Operations (CAFOs) |
| Rio Grande (Leasbu Dam to one mile below Percha Dam) | Rangeland Grazing, Permitted Runoff from Confined Animal Feeding Operations (CAFOs) |
| Rio Grande (Picacho Bridge to Leasbu Dam) | Rangeland Grazing, Permitted Runoff from Confined Animal Feeding Operations (CAFOs) |
| Mimbres: | |
| Bear Canyon Reservoir | Rangeland Grazing |
| Mimbres R (Perennial reaches downstream at Willow Springs) | Rangeland Grazing, Irrigated Crop Production |
| Mimbres R (Perennial reaches Willow Springs to Cooney Cny) | Rangeland Grazing |
| Pecos Headwaters: | |
| Bull Creek (Cow Creek to headwaters) | Rangeland Grazing |
| Cow Creek (Bull Creek to headwaters) | Rangeland Grazing |
| Cow Creek (Pecos River to Bull Creek) | Rangeland Grazing |
| Gallinas River (Las Vegas Diversion to headwaters) | Rangeland Grazing |
| Pecos River (Canon de Manzanita to Alamitos Canyon) | Rangeland Grazing |
| Pecos River (Santa Rosa Reservoir to Tecolote Creek) | Rangeland Grazing |
| Pecos River (Sumner Reservoir to Santa Rosa Reservoir) | Rangeland Grazing |
| Pecos River (Tecolote Creek to Canon de Manzanita) | Rangeland Grazing |
| Tecolote Creek (I-25 to Blue Creek) | Rangeland Grazing |
| Wright Canyon Creek (Tecolote Creek to headwaters) | Rangeland Grazing |
| Rio Hondo: | |
| Alto Lake, Pesticide Application | Pesticide Application |
| Rio Ruidoso (Rio Bonito to US Hwy 70 Bridge) | Rangeland Grazing |
| Rio Ruidoso (US Hwy 70 Bridge to Mescalero Apache bnd) | Rangeland Grazing |
| Rio Penasco: | |
| Rio Peñasco (HWY 24 to headwaters) | Rangeland Grazing |
| Rio Peñasco (Pecos River to HWY 24) | Rangeland Grazing |
| Upper Pecos-Black: | |
| Pecos River (Black River to Tansil Lake) | Rangeland Grazing, Irrigated Crop Production |
| Pecos River (TX border to Black River) | Rangeland Grazing |
| Upper San Juan: | |
| Gallegos Canyon (San Juan River to Navajo bnd) | Irrigated Crop Production |
| San Juan River (Animas River to Cañon Lao) | Rangeland Grazing |
| Animas: | |
| Animas River (Estes Arroyo to CO border) | Rangeland Grazing, Irrigated Crop Production |
| Middle San Juan: | |
| La Plata River (McDermott Arroyo to CO border) | Rangeland Grazing, Animal Feed Operations(NPS) |
| La Plata River (San Juan River to McDermott Arroyo) | Rangeland Grazing, Animal Feed Operations(NPS) |
| San Juan River (Navajo bnd at Hogback to Animas River) | Rangeland Grazing |
| Upper Gila: | |
| Black Canyon Creek (East Fork Gila River to headwaters) | Rangeland Grazing |
| Lake Roberts | Agriculture |
| Taylor Creek (Beaver Creek to Wall Lake) | Rangeland Grazing |
| Taylor Creek (Perennial reaches abv Wall Lake) | Rangeland Grazing |
| Wall Lake | |
| Upper Gila-Manges: | |
| Mangas Creek (Gila River to Mangas Springs) | Rangeland Grazing |
| San Francisco: | |
| Centerfire Creek (San Francisco R to headwaters) | Rangeland Grazing |
| Negrito Creek (South Fork) | Rangeland Grazing |
| Negrito Creek (Tularosa River to confl of N and S forks) | Rangeland Grazing |
| San Francisco River (Centerfire Creek to AZ border) | Rangeland Grazing |
| Tularosa River (San Francisco R to Apache Creek) | Rangeland Grazing |
| Source of information: 2006-2008 State of NM Clean Water Act 303d&305b Integated List |
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