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The ecology of phytoplankton reservoir communities plays a pivotal role in their management and in the development of inland fisheries in the water scarce semi-arid regions of Rio Grande do Norte State, Brazil. The hydrological conditions characterizing these reservoirs include infrequent rainfall and high evaporative loses. The phytoplankton assemblages in tropical climate are structured primarily on dry and wet cycles, not the annual temperature and light regime. The purpose of the current study was to investigate the ecological aspects of phytoplankton communities from three reservoirs during the period of July 2003-June 2004, which include atypical summer rainfall and reservoir overflow. The environmental data broadly divided into two categories, stress factors and disturbance factors. The stress factors deals with the impact of high particulate organic matter and low dissolved oxygen concentrations and disturbance factors, linked to water level fluctuation through flushing and reservoir drawdown, and these events are associated with the phytoplankton assemblages. Results indicated that the three distinct hydroperiods determined the structure of phytoplankton and chlorophyll levels and limited the presence and relative abundance of cyanobacterial species. Phytoplankton succession accompanied changes in clear and turbid water phase represented by the alternate dominance between diatoms and chlorophytes. Inundation and complete filling of reservoir stimulated "s" and "r" strategists species (<20 um) of unicellular and some colonial members of chlorophytes and cryptomonads in highly turbid water environment, and "c" strategist species in rest of the wet period following disturbance gradients. Statistical analysis elicited a significant relationship between particulate organic matter and relative abundance of smaller chlorophytes, which was deemed as stress factor. The flushing and reservoir drawdown indicate disturbance gradient and as a consequence high diversity. Furthermore, a substantial reduction in chlorophyll levels was registered in turbid water phase is related to the reduction of light penetration and re-suspension of sediments. Considering these results, it can be suggested that the well-managed reservoir drawdown can possibly maintain an environment free of eutrophication and cyanobacterial dominance. (C) 2009 Elsevier GmbH. All rights reserved.