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This dataset contains macroinvertebrate community data collected from riffle habitats in eight tropical headwater streams located in Ubatuba, São Paulo State, Brazil. The data were used to assess the effects of Bacillus thuringiensis israelensis (BTI), applied for blackfly control, on macroinvertebrate abundance, taxonomic richness, functional feeding groups, and food‑web structure. Sampling was conducted in two consecutive years (2015 and 2016), during which each stream was divided into an untreated upstream control stretch and a downstream stretch treated with BTI. Within each stretch, multiple sampling sites were surveyed, and benthic macroinvertebrates were identified to the lowest feasible taxonomic level (typically morphospecies) and assigned to functional feeding groups (e.g. predators, collector‑filterers, collector‑gatherers, shredders, scrapers). The dataset includes raw site‑level observations as well as stream‑level summaries used in paired statistical analyses comparing treated and control reaches. These data support univariate tests of abundance and richness, multivariate analyses, and structural equation models evaluating direct and indirect food‑web responses to BTI application. All analyses were conducted in R, and accompanying scripts are provided to ensure full reproducibility of the results reported in the associated publication. This dataset supports the manuscript "The effects of Bacillus thuringiensis var. israelensis (BTI) on tropical stream food webs vary between two consecutive dry seasons", currenty under review in the journal Insect Conservation and Diversity.