Ecological filtering and exaptation are related concepts in which prior traits and adaptations facilitate transitions to new habitats or niches, sometimes by being co-opted for a new function. I investigated possible ecological filtering/exaptation in Percidae, a family of freshwater fishes that shows its highest species richness in small benthic fishes living in creeks and small streams. I hypothesize that traits associated with transitions to benthic living subsequently facilitated the colonization of small river habitats. Using phylogenetic comparative approaches, I found that transitions in river size were dependent on presence or absence of a gas bladder, and long-term residency in small rivers in particular was associated with transitions to benthic living. Based on body size and 3D whole body shape datasets, I found that selection towards smaller bodies and longer caudal peduncles in benthic species in large rivers appears to have enabled transitions to small rivers, while also slowing rates of shape and size evolution; this may explain the high proportion of small, benthic darters. Contrasting selective pressures from habitat exaptation and trophic adaptations in small rivers may constrain ecomorphological diversification. Overall, ecological filtering and/or exaptation may impact both the biodiversity and phylogenetic composition of fish assemblages in small streams.