Toxic cyanobacteria are common in Portuguese freshwaters and are a cause of concern, given that exposure to subacute levels of cyanobacterial toxins through drinking and recreational water might have deleterious effects on human health. Since 1996 several laboratories have been involved in the screening of cyanotoxins in different freshwater bodies, some on a regularly basis but most on a sporadically basis. Here we present data on the phytoplankton communities and on microcystins production occurring in six freshwater reservoirs located in a dry region of south Portugal, from May to December 2005 and April to July 2006. Most of the reservoirs experienced cyanobacterial blooms of various intensities, following noticeable shifts in phytoplankton composition towards cyanobacterial dominance. The seasonal dominance of cyanobacteria during warmer periods was not a fi xed pattern since considerable amounts of cyanobacteria were also recorded during winter months in some reservoirs. Microcystins were detected in 23% of the 53 samples tested and some of them had concentrations higher than the WHO guideline of 1μg L-1 of microcystins, but their amounts not always reflected the encountered cyanobacteria biomass. Although Microcystis aeruginosa seems to be the major species responsible for microcystins production, other potentially toxigenic bloom-forming species were also found. These results reflect the irregular and unpredictable nature of cyanobacterial blooms in what respects to their occurrence, their composition, their intensity and persistency, as well as to their overall toxicity, strengthening the need of a systematic survey of freshwater resources for the correct risk assessment of cyanobacteria and associated toxins in natural environments.