New methods are required for biomonitoring of poorly known tropical ecosystems, but biological assessments of environmental status are limited by insufficient information on taxonomy, composition, and ecology of local communities. The current work applies DNA-based assessment to establish the impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in an understudied biodiversity hotspot in South Asia, an area that attracts increasing attention for the loss of aquatic ecosystems. We sampled 16 river systems...