This document is a doctoral thesis presented by Paula Yuri Nishimura to the Biology Institute at the University of São Paulo. The thesis investigates the phytoplankton community in the Billings and Guarapiranga reservoirs in the São Paulo Metropolitan Area using a functional groups approach. Due to unexpected issues during data collection, the focus shifted from the planned study of cyanobacteria transfer between the reservoirs to characterizing the phytoplankton community and an invasive dinoflagellate, Ceratium furcoides, found in both reservoirs. Additional sampling was conducted to examine spatial heterogeneity in the Guarapiranga reservoir. The thesis contains 6 data chapters presenting the results and a final chapter with overall conclusions.