The protection of riparian zones is critical for biodiversity conservation. The exclusion of human activities and invasive nonnative fish species have been used as measures to protect vulnerable native fish populations in Bonita Creek, Graham County, Arizona. The abundance of 5 native fish species, during 2005–2016, and mesohabitat proportions, during 2011–2016, were estimated at 4 sites to assess the effectiveness of these conservation measures. Interannual variation in numbers was high for all the species, with the speckled dace (Rhinichthys osculus) being the most abundant. The speckled dace significantly increased at one of the sites; the Sonora sucker (Catostomus insignis) significantly decreased at 2 sites; and the longfin dace (Agosia chrysogaster), the desert sucker (Catostomus clarkii), and the Gila chub (Gila intermedia) populations did not display any significant trend. Correlations between fish abundance and mesohabitat proportions were highly variable but mostly nonsignificant. These results suggested that conservation efforts contributed to the stabilization of native fish populations. However, current trends and especially the partial decline of the Sonora sucker emphasized the need for further monitoring and research that would allow managers to better understand fish population dynamics and ecology and ultimately achieve the full recovery and conservation of native fish populations and their habitats.