Natural ecosystems often show highly productive habitats that are clustered in space. Environmental disturbances are also often nonrandomly distributed in space and are either intrinsically linked to habitat quality or independent in occurrence. Theoretical studies predict that configuration and aggregation of habitat patch quality and disturbances can affect metacommunity composition and diversity, but experimental evidence is largely lacking. In a metacommunity experiment, we tested the effects of spatially autocorrelated disturbance and spatial aggregation of patch quality on regional and local richness, among-community dissimilarity, and community composition. We found that spatial aggregation of patch quality generally increased among-community dissimilarity (based on two measures of β diversity) of communities containing protozoa and rotifers in microcosms. There were significant interacting effects of landscape structure and location of disturbances on β diversity, which depended in part on the specific β diversity measures used. Effects of disturbance on composition and richness in aggregated landscapes were generally dependent on distance and connectivity among habitat patches of different types. Our results also show that effects of disturbances in single patches cannot directly be extrapolated to the landscape scale: the predictions may be correct when only species richness is considered, but important changes in β diversity may be overlooked. There is a need for biodiversity and conservation studies to consider the spatial aggregation of habitat quality and disturbance, as well as connectivity among spatial aggregations.