In recent decades, there have been frequent occurrences of the cyanobacterium Cylindrospermopsis raciborskii in northeastern Brazil. Little is known regarding the response of straight and coiled morphotypes to environmental conditions such as light intensity and water temperature. Samples were collected at the Mundaú reservoir (PE, Brazil) at six sampling depths in the dry and rainy season. Both morphotypes exhibited seasonal and vertical differences in densities. The reservoir was stratified in the dry season, with a predominance of the straight morphotype. The coiled morphotype exhibited greater densities in the lower strata and prove to be more susceptible to light. There was evident thermal de-stratification in the rainy season, with a predominance of the coiled morphotype in the surface layers. Thermal de-stratification favors an increase in both morphotypes by providing adequate conditions for growth, such as low light intensity and milder temperatures, which are characteristic of the winter season in the northeastern Brazil.