Potamoplankton attracts little research attention worldwide and this also holds true in Brazil, despite its numerous river systems. The origin and maintenance of phytoplankton populations in these systems have not been well studied. We analysed biological, physical and chemical parameters of the Paraibuna and Pomba rivers to identify the main driving forces behind temporal and spatial phytoplankton patterns. Both systems are located in the southeast, the most populated region. These rivers are similar in climate and geomorphology, and have become eutrophic due to the increase in the human population of the region, especially in Paraibuna River catchments. Twelve and eleven stations were, respectively, sampled during the dry and rainy seasons in the Paraibuna and Pomba rivers. The seasonal pattern of abiotic and biotic variables was related to the increase in the discharge and dilution caused by the rainy period. However, human influences such as the presence of a reservoir and sewage inflow were important to distinguish the rivers. The phytoplankton community of Paraibuna River was influenced by Chapéu D'Uvas Reservoir, which was dominated by a toxic population of Cylindrospermopsis raciborskii. Pomba River phytoplankton was typical of the lotic tropical systems. Phytoplankton functional groups in both rivers were those commonly found in turbid and turbulent shallow lakes. Although the functional group approach was originally described for lentic environments, our data support this approach for lotic community patterns. PHYTOPLANKTON DYNAMICS IN TROPICAL RIVERS Figure 5. Principal Component Analysis based on data from the Paraibuna and Pomba rivers during the dry and rainy periods. WT ¼water temperature, Cond: electrical conductivity, Turb ¼ turbidity, DO: dissolved oxygen, TP: total phosphorus, SRP: soluble reactive phosphorus, SRSi: soluble reactive silica, DIN: dissolved inorganic nitrogen, Chlo: chlorophyll -a, Bact: bacterioplankton. Numbers indicate sample sites