Context dependency is an emerging topic that is challenging our understanding of the factors shaping biodiversity in metacommunities. River networks and other dendritic systems provide unique systems for examining variation in the processes shaping biodiversity between different metacommunities. We examined biodiversity patterns in five benthic invertebrate data sets, from two catchments in central Germany, with the aim of exploring context dependency in these systems. We used variance partitioning to disentangle the variation explained in three biodiversity metrics: taxonomic richness, Simpson’s diversity and local contribution to beta diversity (LCBD; a measure of the uniqueness of a site). As explanatory variables, we used proxies of network position (i.e. catchment size and altitude) and habitat conditions. Contrary to our expectation, we found no evidence of a decline in LCBD downstream in our study. Local habitat conditions and catchment land use played a much stronger role than catchment size and altitude in explaining variation in the three biodiversity metrics. Observed patterns were highly variable between different data sets in our study. These findings suggest that factors shaping biodiversity patterns in these systems are highly context dependent and less related to their position along the river network than local habitat conditions. Given the clear context dependency between data sets, we urge researchers to focus on disentangling the factors driving the high levels of variability between individual systems through the study of a number of replicate, rather than single, metacommunities.