Beta diversity has become essential for understanding ecosystem functioning and for determining biodiversity-conservation priority areas. However, the beta diversity patterns of invertebrates in tropical aquatic ecosystems are not well known, particularly in streams. Using data from low-order streams located in southern Brazil, we evaluated the beta diversity of Chironomidae. We tested the hypothesis that increased environmental heterogeneity increases beta diversity. The streams were grouped into two categories, rural and urban, according to the percentage of urbanization in their micro-basins. Our results showed that the heterogeneity of environmental variables can determine the beta diversity of Chironomidae, and the increased environmental heterogeneity caused by differences in the intensity of urbanization impacts can increase the beta diversity in urban streams. Therefore, the intensified impacts of anthropogenic activities in aquatic ecosystems can also increase beta diversity. Finally, we suggested that beta diversity can be an effective tool for not only designing measures and determining priority conservation areas, but also accurately identifying potentially degraded and priority sites that require water management plans.