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The toxicity of pollutants on aquatic communities is determined by the specific sensitivities and by the ecological relationships between species, although the role of ecological interactions on the specific sensitivity to pollutants is complex. We tested the effect of exposure to copper on the life-history strategies of two coexisting rotifer species of the genus Brachionus from Inca-Coya lagoon, an isolated water body located in Atacama Desert. The experiments looked at differences in the response to the stress by chemical pollution mimicking field conditions of copper exposure, levels of food, and salinity, between single-species cultures and coexisting species. Under single species cultures, B. ’Nevada’ had lower densities, growth rates, and resting eggs production than B. quadridentatus; when in competition, B. ’Nevada’ performed better than B. quadridentatus in most life-history traits. B. ’Nevada’ was a copper-tolerant species, which outcompeted B. quadridentatus, more copper-sensitive, with higher levels of copper. Species-specific responses to environmental conditions and pollution, plus differential relationships between population density and production of resting eggs, resulted in reduced niche overlap between species, allowing stabilized coexistence. The extreme environmental conditions and the isolation of the Inca-Coya lagoon, make it an excellent model to understand the adaption of aquatic organisms to stressed environments.