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The Volcán River watershed in the south Pacific of Costa Rica comprises forests, small urban settlements, cattle fields, and intensive agriculture (mostly pineapple and sugarcane). The ecological integrity and quality of its waters was assessed from 2011–2013 and 2018–2019 by means of physical–chemical parameters (pH, conductivity, temperature, DO, DBO, nitrate, total phosphorus, and pesticide residues) and benthic macroinvertebrate (MI) sampling in eight sites (Volcán, Cañas, and Ángel Rivers, and Peje and Maura streams), resulting in high ecological integrity in all sites except the Peje stream, which is polluted with nitrates and pesticides. Only in this stream was there a marked seasonal variation in the abundance of 16 MI families including Leptohyphidae, Leptophlebiidae, Philopotamidae, Glossossomatidae, and Corydalidae, among others, whose presence was limited exclusively to the dry season (December to April), disappearing from the stream in the rainy season, with corresponding peaks in nitrate (max 20.3 mg/L) and pesticides (mainly herbicides and organophosphate insecticides). The characteristics of the watershed, with large areas of forest and excellent water quality, allow for the re-colonization of organisms into the Peje stream; however, those organisms are incapable of development and growth, providing evidence of a contaminant-driven habitat fragmentation in this stream during the rainy season.