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.