Habitat stability is an important driver of ecological community composition and development. River epilithic biofilms are particularly unstable habitats for the establishment of benthic communities because they are regularly disturbed by floods. Our aim was to determine the influence of habitat instability on meiobenthic organisms. We hypothesized that hydrologic variables are the most important predictors of meiofauna distribution. We monitored epilithic communities (meiofauna and microalgae) with a high sampling frequency during 2 sampling periods with contrasting hydrodynamic patterns in a temperate river (the Garonne, France). Nematodes and rotifers dominated meiofaunal assemblages. The critical flow velocity threshold for their maintenance in the biofilm was ∼30 cm/s, a result suggesting that meiofauna can resist higher flow velocity within the biofilm than within sediments. Nematode distribution was primarily influenced by the duration of undisturbed periods, whereas rotifer distribution was also correlated with the thickness of the biofilm. During the periods after floods, rotifers were faster colonizers than nematodes. Collectively, our results show that flow regime was an essential driver for biofilm community development.