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• Indian freshwater ecosystems are not well studied, are degraded due to expansive agriculture and are contaminated with pesticides. • Mesocosms identified malathion was the dominant stressor among co-occurring stressors. • In mesocosms malathion reduced richness, organism densities and caused community homogenisation. • Toxicology test comparisons between countries identify that Indian taxa may be relatively pesticide tolerant. Globally, river pesticide concentrations are associated with regional and local stream invertebrate diversity declines. Pesticides often co-occur with elevated nutrients (e.g. nitrogen and phosphorus) and sediments related to agriculture, making their individual effects difficult to disentangle. These effects are also less well studied in Asia, than in other geographic regions. Within Asia, India is one of the largest producers and users of pesticides and has approximately 60% of total land mass used for agriculture. Here we examine the responses of Indian river invertebrate communities subjected to malathion, nutrients, and sediment additions in a semi-orthogonal design, in three sequential (through time) short-term (120 h) mesocosm experiments. Additionally, a series of single-species toxicity tests were run that used 24 h exposure and 72 h recovery to examine the sensitivity of 13 local invertebrate taxa to malathion, and 9 taxa to cypermethrin, comparing these results to those from other biogeographic regions. Mesocosm results indicate that malathion exposure had a major effect compared to other stressors on communities, with a lesser effect of nutrients and/or sediments. In mesocosms, taxa richness, total abundance and the abundance of sensitive species all declined associated with malathion concentrations. Comparisons of organism sensitivities from other geographic locations and those in the current paper suggest taxa in India are relatively tolerant to malathion and cypermethrin. Our results further reinforce that the high observed aquatic pesticide concentrations known to occur in Asian freshwater ecosystems are likely to be negatively affecting biodiversity, homogenising biota towards those most stress tolerant. [ABSTRACT FROM AUTHOR]