The changes related to major phytoplankton groups, even though they were not significant, showed that Cyanobacteria were more abundant in neutral periods, while Chlorophyceae dominated La Nina phase and Bacyllariophyceae dominated El Nino. It was also possible to observe changes in morphology that dominated the phytoplankton at different periods; during La Nina and neutral cycles the development of colonial forms increased, mainly Chlorococcales and Chroococcales groups. This morphological type is functionally related to a more stable condition in the water column (Reynolds, 2006; Huisman et al., 2005). During periods of El Nino, with greater instability in the water column, filamentous forms were dominant, being better adapted to the higher flow rate and increased turbulence accompanied by an increased incidence of winds.