AbstractThe identification of the mechanisms underlying patterns of species co‐occurrence is a way to identify which process(es) (niche, neutral, or both) structure metacommunities. The current paper had the goal of identifying patterns of co‐occurrence in Neotropical stream fish and determining which processes structure the fish metacommunity, and identifying any gradients underlying this structure. Results indicated that the metacommunity formed by the species pool was structured by a pattern of nested co‐occurrence (hyperdispersed species loss) and a mass‐effect mechanism. However, a set of core species, displaying a Clementsian pattern, was structured by a species‐sorting mechanism. Both, hyperdispersed species loss and the Clementsian patterns point to a discrete set of communities within the metacommunity. These communities could be isolated by the water physicochemical conditions or morphological characteristics of the stream channel.