The São Francisco River, located in the main hydrographic basin of the semiarid region of Brazil, has seven dams along its course, built for electric power generation (ANA, 2013). The present study was conducted for two consecutive years, and two reservoirs (Xingó and Itaparica) were monitored in order to characterize the phytoplankton community in these environments, through the analysis of taxonomic composition, an important tool commonly used in monitoring programs to assess water quality worldwide.