We investigated the biomass, primary productivity, species diversity and their controlling factors in the deeper region of the Barra Bonita reservoir (22°29S and 48°34W) in the State of São Paulo, Brazil. To accomplish this, short term changes (days and month) were measured during two periods of the year, winter 1993 and summer 1994. The response of the phytoplankton communities to the variability of the system, taking into account the Intermediate Disturbance Hypothesis (IDH), indicated that the frequency and intensity of the disturbances have a critical influence on the establishment of the communities. In Barra Bonita Reservoir the conditions for mixing in the winter were probably important for maintaining high diversity. On the other hand, in summer, the concentrations of suspended material, the high temperatures, and the greater stability of the water column, were probably responsible for permitting the establishment of Microcystis aeruginosa.