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Context dependency is a key challenge emerging in metacommunity ecology, which is hindering the development of general ecological theories. 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 datasets, from two drainage basins 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, including the local contribution to beta diversity (LCBD; a measure of the uniqueness of a site), by proxies of network position (i.e. catchment size and elevation) and local environmental conditions. Contrary to 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 elevation in explaining biodiversity metrics. Observed patterns were highly variable between different datasets 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 datasets, we urge researchers to focus on disentangling the factors driving the high levels of variability between individual systems through the simultaneous study of a number of replicate metacommunities.