AbstractObjectiveThe Colorado River has undergone substantial anthropogenic modifications, and a suite of nonnative species have been introduced since the 1800s; consequently, native fish communities are severely imperiled. We examined temporal patterns in fish community structure in Lake Mohave (i.e., lower Colorado River basin) over 40 years from 1980 to 2020.MethodsWe examined long‐term abundance and richness trends and the trajectory of fish community structure in multivariate space to assess stability and turnover using results from biannual (spring and autumn) trammel‐net monitoring over 40 years from 1980 to 2020.ResultNonnative fishes were established prior to sampling, precluding the ability to determine historical fish community structure. Bonytail Gila elegans and Razorback Sucker Xyrauchen texanus were the only two remaining native fishes, and both declined precipitously in abundance through time. However, a repatriation program initiated in 1991 prevented Razorback Sucker from extirpation, while reintroduction efforts for Bonytail have failed. Both wild populations are gone. Total catch per unit effort showed a negative relationship from 1980 to 2020, whereas total species richness showed no relationship. Long‐term abundance trends at the species level indicated three nonnative species (i.e., Gizzard Shad Dorosoma cepedianum, Yellow Bullhead Ameiurus natalis, and Smallmouth Bass Micropterus dolomieu) increased, nine decreased, and three showed no relationship. Fish community composition exhibited low stability and moderate turnover and shifted directionally through time in multivariate space, with the formation of three clusters, possibly indicating alternative states.ConclusionThe contemporary fish community shows little resemblance to the endemic ichthyofauna that has historically occupied the Colorado River, and the Razorback Sucker is the only remaining native species due to recovery efforts. Continued adaptive management will be required to preserve the most genetically diverse Razorback Sucker population in the Colorado River system, especially while coexisting with an unstable nonnative fish community.