Resumo. Abstract: Aim The study analyzed the potential use of the phytoplankton functional groups as an environmental bioindicator in aquatic ecosystems of Brazilian semiarid region. Methods Using data collected over five years of a natural lagoon and two reservoirs, we evaluate the relationship between functional groups and environmental conditions through the multivariate approach. The Q index was applied to assess ecological status in these ecosystems. Results In Panati, the temporary and natural lagoon, the partial habitat desiccation and presence of macrophytes reflected in the less nutrients concentrations and phytoplankton composition, with high biomass of coccoids Chlorophyceae, diatoms and desmids (functional groups J, MP and N, respectively). Taperoá and Soledade reservoirs presented high cyanobacteria contribution, however the biomass and contribution of cyanobacteria in Taperoá (SN, S1) were lower than in Soledade. In this reservoir, cyanobacteria were more abundant, alternating in dominance (LO, M, LM, SN, S1). According to tendencies revealed by Redundancy Analysis (RDA), the main driving abiotic factors on the phytoplankton functional groups were pH, nutrients and light availability. As expected, phytoplankton composition directly influenced the Q index result, showing mostly bad to tolerable conditions in Soledade, medium to good in Taperoá and good to excellent in Panati. Conclusions The Q index was a good tool to assess the water quality and ecological status in aquatic ecosystems from the Brazilian semiarid region, reflecting the influence of natural control mechanisms on the harmful cyanobacteria blooms in temporary ecosystems.