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Aquatic communities vary depending on local factors, such as environmental conditions and biological interactions and regional factors, such as the hydrological regime in floodplains. This study analyzed the community structure of rotifers and their secondary production in two lakes of an Upper Paraná River floodplain (Brazil) differing in their hydrology: one connected to the river and the other isolated. Integrated samples of the water column were collected daily during 15 days in the low and high water periods. Three statistical methods, ANOVA, MRT, and IndVal were applied to distinguish the structure, biomass, and secondary production of their rotifer communities. The rotifer fauna was rich (91 species). Temperature, an indicator of seasonal change, and hydrological connection to river were major factors structuring rotifer communities. The community presented differences between periods in the isolated lake, but had a higher stability in the connected lake. We identified 34 indicator species of the groups formed by the MRT analysis. Production was low and consistent in the connected lake (∼1.5 µg DW m−3 day−1), being higher and more variable in the isolated lake (peaking at ca. 60-90 µg DW m−3 day−1). Results also showed that changing environmental conditions verified in the low water period and in the isolated lake were determinant for both the community structure and the secondary production of rotifers. We demonstrate that not only flooding but also the levels of isolation from the river during low water period are the driving forces for the structure and dynamics of organisms in floodplains. Thus, the isolated lakes represent important areas for rotifer biodiversity. [ABSTRACT FROM AUTHOR]