Spatial position within a dendritic network may determine environmental filters and connectivity with source of immigrants, influencing species composition and variation in metacommunities. We investigated how long-term turnover of riffle-dwelling fish assemblages is affected by niche- and dispersal-related processes. Multiple linear model selection resulted in four variables important to explain assemblage turnover: (i) habitat change, (ii) channel slope, (iii) dlink (a proxy for connectivity), and (iv) catchment area. These four variables were related to turnover in species abundance, while turnover in species occurrence was only related to habitat change. Models generated for each species indicated they were differently affected by niche- and dispersal-related processes. Our findings provide support for the hypothesis that metacommunity processes affecting temporal turnover of stream fish communities are dependent on the spatial position within a dendritic network, but also vary among species. Our study has implications for sampling design in monitoring programs, as the degree of dissimilarities in fish communities depends not only on local habitat change, but on spatial position within the drainage network and on species particularities.