Theory predicts that different components of species diversity should increase with environmental heterogeneity. Our main aim was to examine the relationship between β-diversity and environmental heterogeneity in a system with high habitat heterogeneity and very small spatial distances between sites. This system allowed us to examine the effect of habitat heterogeneity on β-diversity in the absence of dispersal limitation. We surveyed 100 riffle sites (10 riffles in each of 10 streams) for benthic macroinvertebrates in a boreal drainage basin. Streams differed in average community composition (based on canonical analysis of principal coordinates) and heterogeneity in community composition (based on test of homogeneity of dispersion). These results were robust regardless of the distance measures used in distance-based multivariate analyses. β-diversity was not significantly correlated with stream habitat heterogeneity, despite the fact that the latter was quantified by a large set of environmental variables deemed important for species occurrence in our study streams. Thus, we suggest that the relationship between β-diversity and habitat heterogeneity was masked by individual species–environment responses and mass effects. Thus, the β-diversity–habitat heterogeneity relationship may not always be significant, a result that may have important consequences for understanding the structure of community patterns. Despite the absence of a significant β-diversity–habitat heterogeneity relationship, community structure was significantly associated with environmental factors (e.g., moss cover, stream width, velocity) across the streams in distance-based redundancy analysis. This finding suggests that different ways to associate β-diversity, community structure, and environmental conditions may yield different insights into the structure of biotic communities.