The responses of algae to herbicides depend on the sensitivity of each species, but competition within algal communities may be an important regulator of the effects of herbicides on aquatic systems. The impact of herbicides on algae also depends on abiotic factors like nutrients, light, and temperature. We examined the tolerance of the alga Oscillatoria limnetica Lemmermann to the photosystem II inhibitor herbicide atrazine under different culture conditions to assess those interactions between herbicides and biotic and abiotic factors. The density of the cyanobacterium O. limnetica was determined in natural phytoplanktonic assemblages and in unialgal cultures in medium containing 10 μg/L atrazine. Experiments (total of 13) were conducted in spring and early and late summer, during which the effect of atrazine varied in nature and intensity. The growth of the cyanobacterium was always inhibited in cold experiments, whereas it was stimulated in warm experiments within the natural phytoplankton assemblage, but unaffected in pure culture. Laboratory experiments with unialgal culture showed that the sensitivity to atrazine increased as the temperature decreased. Phytoplankton community structure, interactions between species, and environmental parameters (e.g., temperature) are important factors controlling the responses of cyanobacteria to the herbicide. These interactions between sensitivity to herbicides and environmental factors may reduce or emphasize the effects of pollution in aquatic systems. Thus, the ecotoxicological relevance of herbicides in aquatic systems is quite complex and cannot be assessed by single-species short-term laboratory toxicological tests.