| Abv Heron LakeHEWN5 | Rio Arriba | - | - | 309 |
| Albuquerque - Paseo Pump StationPPSN5 | Bernalillo | - | - | 600 |
| Animas River 1 WSW AztecAZRN5 | San Juan | - | - | 368 |
| Animas River at FarmingtonARFN5 | San Juan | - | - | 426 |
| AnzacGNTN5 | Cibola | - | - | 363 |
| Azotea Tunnel Outlet near ChamaCHUN5 | Rio Arriba | - | - | 390 |
| Below Lake AvalonPBAN5 | Eddy | - | - | 407 |
| 5 SSE below Mesilla Dam near MesillaMSLN5 | Dona Ana | - | - | 423 |
| Bernalillo - Jemez RiverJECN5 | Sandoval | - | - | 347 |
| Bernardo 1SW - Rio PuercoBNDN5 | Socorro | - | - | 407 |
| Black River Malaga 1NEMGAN5 | Eddy | - | - | 436 |
| Black River Malaga 5WMLAN5 | Eddy | - | - | 433 |
| Bloomfield - San Juan RiverBFDN5 | San Juan | - | - | 457 |
| Blue Spring 6 E (Blue Spring Whites City 6E)BSSN5 | Eddy | - | - | 322 |
| Canadian River 2 S Taylor SpringsTYLN5 | Colfax | - | - | 407 |
| Canadian River 3 NE SanchezSNCN5 | San Miguel | - | - | 322 |
| Canadian River at LoganLCRN5 | Quay | - | - | 407 |
| Carlsbad North 3NNW Main CanalCMCN5 | Eddy | - | - | 235 |
| Casias Crk near CostillaCCCN5 | Taos | - | - | 217 |
| Cimarron River 3 SE (Eagle Nest)EGCN5 | Colfax | - | - | 322 |
| Cimarron River 4 W CimarronCMMN5 | Colfax | - | - | 322 |
| Costilla 16SE - Costilla CreekCBDN5 | Taos | - | - | 407 |
| Costilla Creek 1 N CostillaCCSN5 | Taos | - | - | 322 |
| Costilla Creek 2 SE CostillaCOSN5 | Taos | - | - | 322 |
| Costilla Crk above Costilla DamCCAN5 | Taos | - | - | 225 |
| Cowles - Rio MoraRMON5 | San Miguel | - | - | 440 |
| Coyote Creek 2 NE GolondrinasCYCN5 | Mora | - | - | 217 |
| Dark Canyon Draw 8 N (Dark Canyon)DKCN5 | Eddy | - | - | 246 |
| Dark Canyon Draw at Dark Canyon CarlsbadDACN5 | Eddy | - | - | 936 |
| Delaware River Red Bluff 11NWRDBN5 | Eddy | - | - | 235 |
| Dunken - Rio PenascoRPDN5 | Chaves | - | - | 440 |
| El Rancho 6SW - Rio GrandeBUKN5 | Santa Fe | - | - | 267 |
| Embudo - Rio GrandeEMBN5 | Rio Arriba | - | - | 407 |
| Embudo Creek 2 NW DixonDIXN5 | Rio Arriba | - | - | 290 |
| Ensenada - Rio BrazosRFRN5 | Rio Arriba | - | - | 320 |
| Farmington - San Juan RiverBRRN5 | San Juan | - | - | 426 |
| Flora Vista - Animas RiverFVAN5 | San Juan | - | - | 235 |
| Fort Sumner Main Canal River GageFSCN5 | De Baca | - | - | 347 |
| Fourmile Draw 4 NNW (Fourmile Draw Lakewood 4NNW)LKWN5 | Eddy | - | - | 322 |
| Galisteo Creek below Galisteo DamRGCN5 | Santa Fe | - | - | 347 |
| Gallinas Creek 2 W MontezumaMTZN5 | San Miguel | - | - | 288 |
| Gallinas River 6 NW ColoniasCOLN5 | Guadalupe | - | - | 230 |
| Gila Hot Springs - Gila RiverEFGN5 | Grant | - | - | 288 |
| Gila Hot Springs - MF Gila RiverMFGN5 | Catron | - | - | 246 |
| Gila River 10 E VirdenGVRN5 | Grant | - | - | 233 |
| Gila River 5 NE RedrockRGRN5 | Grant | - | - | 368 |
| Gila River 7 NE GilaGILN5 | Grant | - | - | 235 |
| Holman - La Sierra DitchLSDN5 | Mora | - | - | 230 |
| Hope - Rio PenascoRPHN5 | Chaves | - | - | 440 |
| Jemez River 3 N Jemez PuebloJEZN5 | Sandoval | - | - | 347 |
| La Plata River at La PlataLPRN5 | San Juan | - | - | 368 |
| La Plata River near FarmingtonLPFN5 | San Juan | - | - | 450 |
| Las Vegas - Gallinas RiverLOUN5 | San Miguel | - | - | 322 |
| Lincoln 4WNW - Rio BonitoRBNN5 | Lincoln | - | - | 359 |
| Maxwell - Eagle Tail DitchETDN5 | Colfax | - | - | 450 |
| Mimbres River at MimbresMIMN5 | Grant | - | - | 217 |
| Mogollon Creek 14 N (Cliff 14N)MCCN5 | Grant | - | - | 582 |
| Mora River 1 E GolondrinasGOLN5 | Mora | - | - | 235 |
| Mora River at La CuevaLCVN5 | Mora | - | - | 391 |
| North Fork Eagle Creek 3WNW AltoECNN5 | Lincoln | - | - | 359 |
| Nps West Fork Gila RiverWFGN5 | Catron | - | - | 234 |
| Pecos River 10 S Malaga 10SRBFN5 | Eddy | - | - | 449 |
| Pecos River 11 NW (Below Brantley Dam)PSBN5 | Eddy | - | - | 217 |
| Pecos River 11 SE (Fort Sumner)PBTN5 | De Baca | - | - | 290 |
| Pecos River 12 NW (Fort Sumner)PSDN5 | De Baca | - | - | 347 |
| Pecos River 15 E DunlapDLPN5 | De Baca | - | - | 290 |
| Pecos River 2 E Carlsbad 2E below Dark CanyonCPDN5 | Eddy | - | - | 290 |
| Pecos River 2 SE Anton ChicoATCN5 | Guadalupe | - | - | 235 |
| Pecos River 3 ESE Lake ArthurLATN5 | Chaves | - | - | 440 |
| Pecos River 3 SE Malaga 3ESEMLGN5 | Eddy | - | - | 407 |
| Pecos River 5 SW AcmeACMN5 | Chaves | - | - | 363 |
| Pecos River 6 E Artesia 6EATSN5 | Eddy | - | - | 440 |
| Pecos River 6 ESE (Pierce Canyon Crossing 6ESE Malaga)PPCN5 | Eddy | - | - | 322 |
| Pecos River 6 N (Santa Rosa)SRDN5 | Guadalupe | - | - | 402 |
| Pecos River 6 NE (Lakewood 6NE - Kaiser Channel)PKCN5 | Eddy | - | - | 322 |
| Pecos River 8 NW Carlsbad 9NW (Damsite 3)CSBN5 | Eddy | - | - | 436 |
| Pecos River 9 N PecosPCON5 | San Miguel | - | - | 406 |
| Pecos River 9 NW (Santa Rosa)SRPN5 | Guadalupe | - | - | 455 |
| Pecos River 9 SE Puerto De LunaPUEN5 | Guadalupe | - | - | 322 |
| Pecos River above Canon Del Uta near ColPECN5 | Guadalupe | - | - | 322 |
| Pecos Rvr near Ft.SumnerPFSN5 | De Baca | - | - | 315 |
| Ponil Creek 5 NW CimarronCMRN5 | Colfax | - | - | 455 |
| Rayado Creek 10 SW CimarronCRCN5 | Colfax | - | - | 322 |
| Red River 2 E QuestaRRQN5 | Taos | - | - | 235 |
| Red River 4 SW QuestaRRFN5 | Taos | - | - | 457 |
| Revuelto Creek 2 SE LoganLGNN5 | Quay | - | - | 407 |
| Rio Chama 1 W ChamitaCMTN5 | Rio Arriba | - | - | 405 |
| Rio Chama 13 SW Tierra AmarillaRCEN5 | Rio Arriba | - | - | 740 |
| Rio Chama 22 WNW AbiquiuRCAN5 | Rio Arriba | - | - | 394 |
| Rio Chama 3 SW (La Puente)RLPN5 | Rio Arriba | - | - | 680 |
| Rio Chama 7 WNW AbiquiuAICN5 | Rio Arriba | - | - | 322 |
| Rio GrandeSMCN5 | Socorro | - | - | 551 |
| Rio Grande 1 ENE (San Antonio)RGSN5 | Socorro | - | - | 440 |
| Rio Grande 1 NE (North Floodway Channel near Alameda)ANFN5 | Bernalillo | - | - | 317 |
| Rio Grande 1 NE Cochiti PuebloCTDN5 | Sandoval | - | - | 362 |
| Rio Grande 1 NNE EscondidaRGEN5 | Socorro | - | - | 440 |
| Rio Grande 1 NW (Alameda at Alameda Bridge)RGBN5 | Bernalillo | - | - | 246 |
| Rio Grande 1 S San MarcialSMFN5 | Socorro | - | - | 457 |
| Rio Grande 1 W near Alameda (Paseo Del Norte Bridge)RGAN5 | Bernalillo | - | - | 407 |
| Rio Grande 12 SW TaosTJBN5 | Taos | - | - | 217 |
| Rio Grande 2 N IsletaISLN5 | Bernalillo | - | - | 407 |
| Rio Grande 2 SW San Ildefonso PuebloOTWN5 | Santa Fe | - | - | 393 |
| Rio Grande 3 NE below Elephant Butte Dam near TorCEDBN5 | Sierra | - | - | 394 |
| Rio Grande 4 SW CerroCERN5 | Taos | - | - | 440 |
| Rio Grande at AlbuquerqueABQN5 | Bernalillo | - | - | 322 |
| Rio Grande at below Caballo DamCAAN5 | Sierra | - | - | 211 |
| Rio Grande at below Leasburg DamLBDN5 | Dona Ana | - | - | 345 |
| Rio Grande at Hayners Bridge near RinconRHBN5 | Dona Ana | - | - | 588 |
| Rio Grande at San AcaciaSNAN5 | Socorro | - | - | 322 |
| Rio Grande at State HWY 346 near BosqueRGQN5 | Valencia | - | - | 363 |
| Rio Grande at The Narrows in Elephant Butte LakeEBNN5 | Sierra | - | - | 436 |
| Rio Grande Del Rancho near TalpaRGTN5 | Taos | - | - | 322 |
| Rio Grande Floodway near BernardoRFBN5 | Socorro | - | - | 368 |
| Rio Grande near Bosque FarmsBRGN5 | Valencia | - | - | 363 |
| Rio Hondo 13 SW RoswellRRHN5 | Chaves | - | - | 394 |
| Rio Hondo 18 W RoswellDARN5 | Chaves | - | - | 217 |
| Rio Hondo 3 E RoswellRHRN5 | Chaves | - | - | 426 |
| Rio Hondo above Chavez Canyon near HondoRHHN5 | Lincoln | - | - | 600 |
| Rio Hondo near ValdezVADN5 | Taos | - | - | 422 |
| Rio Lucero 2 E (Arroyo Seco)RLAN5 | Taos | - | - | 407 |
| Rio Nambe 5 SE NambeRNAN5 | Santa Fe | - | - | 551 |
| Rio Nutria 10 NW RamahRNRN5 | Mckinley | - | - | 322 |
| Rio Ojo Caliente 2 S La MaderaLMDN5 | Rio Arriba | - | - | 235 |
| Rio Penasco Dayton 2WNWDAYN5 | Eddy | - | - | 322 |
| Rio Pueblo 6 E PenascoRPPN5 | Taos | - | - | 13 |
| Rio Pueblo De Taos 5 NE TaosRPTN5 | Taos | - | - | 436 |
| Rio Pueblo De Taos 5 WSW TaosTBCN5 | Taos | - | - | 433 |
| Rio Ruidoso at HollywoodRUHN5 | Lincoln | - | - | 308 |
| Rio Ruidoso at RuidosoRRUN5 | Lincoln | - | - | 954 |
| Rocky Arroyo Lakewood 7SCRBN5 | Eddy | - | - | 246 |
| San Antonio - Elmendorf DitchELMN5 | Socorro | - | - | 407 |
| San Francisco River 5 S GlenwoodGSFN5 | Catron | - | - | 817 |
| San Francisco Rvr near ReserveRSFN5 | Catron | - | - | 298 |
| San Juan River 1 NE ArchuletaARCN5 | San Juan | - | - | 225 |
| San Juan River at FarmingtonFRMN5 | San Juan | - | - | 394 |
| San Juan River at ShiprockSHRN5 | San Juan | - | - | 235 |
| Santa Cruz River 1 NW CundiyoCYON5 | Santa Fe | - | - | 290 |
| Santa Fe 1NNW - Rio TesuqueTBGN5 | Santa Fe | - | - | 394 |
| Santa Fe River 5 E (Santa Fe)SFRN5 | Santa Fe | - | - | 290 |
| Santa Fe River above Cochiti LakeSFCN5 | Santa Fe | - | - | 322 |
| Santa Fe Rvr above Mcclure ResvrSFAN5 | Santa Fe | - | - | 235 |
| Santistevan Crk near CostillaSNTN5 | Taos | - | - | 217 |
| South Diversion Channel at AlbuquerqueSDVN5 | Bernalillo | - | - | 525 |
| South Seven Rivers 1 SE (South Seven Rivers Seven Rivers 1SE)SSRN5 | Eddy | - | - | 322 |
| Teseque Creek 4 NNE (Santa Fe)TSQN5 | Santa Fe | - | - | 440 |
| Tularosa Creek 3 W BentTLCN5 | Otero | - | - | 407 |
| Ute Creek 8 NW LoganLOGN5 | Harding | - | - | 320 |
| Valle de Oro - Rio GrandeVDON5 | Bernalillo | - | - | 322 |
| Vermejo River 1 N DawsonDAWN5 | Colfax | - | - | 363 |
| Watrous - Mora RiverWTSN5 | Mora | - | - | 435 |
| Zuni River 2 NE (Black Rock)ZUIN5 | Mckinley | - | - | 322 |