Multiple‐pass removal by use of small‐mesh seines within enclosed areas was performed to estimate numbers of nine small‐bodied fish species at 17 sites in the Pecos River, New Mexico, during October 2007. Site‐level population estimates were most precise for age‐0 red shiners Cyprinella lutrensis (coefficient of variation [CV, calculated as SE/mean] = 0.02–0.06) and least precise for age‐1 and older plains minnow Hybognathus placitus (CV = 0.03–0.42). Site estimates were expanded to derive species‐ and age‐specific population estimates for 284 km of river, including the full range of the threatened Pecos bluntnose shiner Notropis simus pecosensis (101,131 fish; 95% confidence interval = 76,437–125,825; CV = 0.12). Population estimates and species detection from multiple‐pass removal were compared with a closed, comprehensive, single‐pass catch rate index obtained on the first pass of the removal estimate (comprehensive catch per effort [C‐CPE]) and with an open, single‐pass catch rate index (single‐pass catch per effort [S‐CPE]), where a set of representative mesohabitats was seined in proportion to their availability (mean = 12.6 hauls/site). Compared with removal estimates, C‐CPE provided a reliable index of population size for the nine small‐bodied species combined (r2 = 0.90, P = 0.010) but did not perform as reliably for adult Pecos bluntnose shiners (r2 = 0.51) or age‐0 speckled chub Macrhybopsis aestivalis (r2 = 0.70). On average, C‐CPE detected 89% of species at a site, missing predatory species most frequently. By contrast, S‐CPE was a poor index of population size for all species (r2 = 0.16, P = 0.010) and detected an average of 52% of species at a site. The S‐CPE failed to detect the Rio Grande shiner N. jemezanus at 28.5% of sites, the sand shiner N. stramineus at 41.2% of sites, the Pecos bluntnose shiner at 29.4% of sites, and the speckled chub at 23.5% of sites; all of these are small‐boded native species. For applications that require reliable species detection and precise abundance estimates of small‐bodied fishes, the multiple‐pass removal method is recommended.