Riverine flow regimes are naturally dynamic, but become increasingly homogenized following anthropogenic flow alteration. Loss of dynamism disrupts naturally occurring structuring mechanisms within the associated biotic communities, at times causing shifts in composition. Here we considered how stream fish assemblages in two Central Texas rivers changed after alteration of flow regime by either construction of a mainstem, deep storage reservoir or flood-retaining structures. Following impoundment, number of large and small floods increased from 0.81 to 1.07 floods per year (FPY) in the upper Guadalupe River, decreased from 0.84 to 0.42 FPY in the lower Guadalupe River and decreased from 0.87 to 0.7 FPY in the San Marcos River. Historical ichthyofauna data ranging from 1938 to 2006 were used to assess changes in assemblage composition and species abundance. Assemblages did not differ in the upper Guadalupe River (Bray–Curtis index = 37.4%; ANOSIM global R = 0.079, p = 0.08), but did differ in the lower Guadalupe River (25%; global R = 0.409, p < 0.01) and San Marcos River (27%; global R = 0.19, p < 0.01). In general, habitat generalist species dominated assemblages during periods of reduced flood frequencies (i.e. drought of record; following impoundment), whereas regionally endemic species (N = 3) and substrate and broadcast spawning species (N = 5) declined (b1 < 0; α = 0.05). Based on the results from this study, managing flows in the lower Guadalupe River to mimic historical timing of flood pulses might attenuate contemporary disruption of natural assemblage composition. Copyright © 2010 John Wiley & Sons, Ltd.