The relationships between phytoplankton assemblage, disturbance and trophic characteristics were investigated in Guarapiranga Reservoir, which supplies water to approximately 25% of the São Paulo metropolitan region. Two open-water stations were sampled weekly during 1991–92, in order to determine the main factors promoting of Cyanobacterial growth. These were found to include: rainfall-induced nutrient inputs via runoff and percolation from the drainage basin; circulation patterns that favored resurgence of nutrients and transported littoral algae to the open water; senescence of algae (especially Chlorococcales and Zygnemaphyceae) which increased the availability of nutrients in the water column; and high nutrient concentrations during the driest season. Restricting nutrient inputs and controlling eutrophication are necessary if the quality of water supplied from this reservoir is to be improved.