The lower Rio Grande watershed below Falcon Dam has been 95% developed for agriculture, urban, and industrial uses. The river has been extremely altered to make this possible, with the addition of two more downstream dams, a series of five rock weirs, and numerous water diversions. This regulation has resulted in an extremely altered flow regime and fish fauna since the early 1950s. There has been a significant general retreat and decline of primary freshwater fishes over time, and we identified three significantly different faunal groups across the fragmented watercourse. However, the overall species richness of the region did not change significantly over time, likely due to an ongoing upstream intrusion of estuarine and marine-derived taxa, as well as the increase in the number and spread of non-native taxa. Despite no overall change in species richness within the region, we identified a significant trend in the species richness of the two most diverse primary freshwater fish families, Leuciscidae and Centrarchidae. Leuciscid richness significantly declined and centrarchid richness significantly increased over the 68-year period. Fluvial native leuciscid species that require a natural flow regime became extirpated or extinct, while lentic-adapted native and introduced centrarchids have thrived. The flow regime of the lower Rio Grande has been severely altered since impoundment of Falcon Reservoir. Median monthly flows have declined for all months, maximum flows and high flow pulses have declined, and base flows have increased. Also noteworthy were the increased number of hydrograph reversals post-impoundment. The streamflow regime is of central importance in sustaining the ecological integrity of rivers, and its disruption in the lower Rio Grande corresponds to a vastly different contemporary fish fauna than what historically occurred.