-(Phytoplankton in three lateral lakes and in the Paranapanema River in its mouth zone into Jurumirim Reservoir, São Paulo, Brazil, during a long drought period). During a disconnection period (from October 1999 to December 2000 between lateral lakes and the Paranapanema River, the temporal changes on structure of phytoplankton community were examined in samples collected every three months, at the littoral and pelagic zones. A total of 183 algae species was found, being the community predominantly constituted by Chlorophyceae and Bacillariophyceae in the Paranapanema River and in an unique continuously isolated lake; and by Bacillariophyceae and Chlorophyceae in the other two lakes. During the year, a decrease on species richness was only found in the lentic ecosystem with higher connectivity loss. The algae Cryptophyceae were abundant (density higher than mean abundance of phytoplankton) in the three lakes, at both zones and during all the year, except at the littoral zone of the lake with higher loss connectivity in November 1999. In the Paranapanema River, Cryptophyceae predominated during a rainy month (February), being the diversity indexes lower than in the other sampling periods. The severe drought conducted to a significant reduction of volume and surface area of the lakes and, one of them, the isolated lake, was completely extinct in the last study period. Only in this lentic ecosystem, a concentration effect on the abundance of phytoplankton was recorded. The predominance of Cryptomonas brasiliensis Castro, C. Bic. & D. Bic., Chroomonas spp. and Chlamydomonas spp., in the three lakes was attributed to the adverse conditions for the development of other algae. Low depth, great amount of sediments in water ressuspended after windy episodes and, in a consequence, high light extinction were the limiting factors for the algae unadapted to these conditions, despite the adequate nutrient contents. In the Paranapanema River, the temporal alterations on the structure of phytoplankton community appear to be linked to water velocity and flux together with hydrological level.Key words -composition, connectivity, drought, phytoplankton RESUMO -(Fitoplâncton em três lagoas marginais ao Rio Paranapanema e em sua desembocadura no Reservatório de Jurumirim (São Paulo, Brasil) durante um período prolongado de seca). Durante um período de desconexão (de outubro de 1999 a dezembro de 2000) entre lagoas laterais e o Rio Paranapanema, a estrutura da comunidade fitoplanctônica e suas alterações foram examinadas em amostras coletadas trimestralmente nas zonas litoral e pelágica. Um total de 183 táxons de algas foi encontrado, sendo a comunidade predominante constituída por Chlorophyceae e Bacillariophyceae no Rio Paranapanema e em um ambiente lacustre permanentemente isolado, e por Bacillariophyceae e Chlorophyceae em duas outras lagoas. Ao longo do ano, diminuição na riqueza de espécies foi encontrada somente no ambiente lêntico com maior perda de conectividade. Cryptophyceae foi abundante (densidades maior que a d...