Changes in equilibrium states in shallow lakes are associated with disturbances and resilience. The study evaluated the structure and composition of phytoplankton functional groups in two lakes, Lagoa do Paó (turbid waters) and Santa Lúcia (clear waters). Monthly collections of limnological variables and phytoplankton occurred between August 2014 and June 2015 in the pelagic region. The lakes shared five functional groups: K, S1 , X1 , W2 and P, formed by coccoid and filamentous cyanobacteria, coccoid chlorophytes and euglenophytes, and desmids, respectively. The canonical correspondence analysis evidenced a clear separation, highlighting the groups TD, N, W2 and S1 in Santa Lúcia and functional groups composed of potentially toxic cyanobacteria in Lagoa do Paó (SN, Lo), indicating that the submerged macrophyte coverage can act promoting the phosphorous stabilization in the sediment in Santa Lúcia, reducing its contribution to the water column and inhibiting the dominance of the mentioned species. Temperature, pH, phosphorus and light attenuation coefficient influenced the occurrence of H1 , SN, S1 , W2 , X1 , D, and Lo , in the Lagoa do Paó. The composition and structure of the functional groups responded in the two lakes with some functional groups associated with toxic cyanobacteria occurring exclusively in Lagoa do Paó, having also been observed the sharing of some functional groups.