This study evaluated the isotopic composition of three zooplankton species - Notodiaptomus amazonicus (Wright, 1935), Moina minuta Hansen, 1899 and Bosmina hagmanni Stingelin, 1904 - from the Upper Paraná River floodplain. We predicted that there would be isotopic variability among species in the different sampled environments. Samplings were conducted in three lakes from the Baía subsystem and in two lakes from the Paraná subsystem. At each location, some abiotic variables were measured, and zooplankton (3 to 4) and phytoplankton (3) samples were taken. The species sampled did not present significant differences between subsystems; however, they were different among the lakes, with variations of about 10.8‰ for δ13C and 5.8‰ for δ15N. The isotopic values found for phytoplankton also did not differ significantly among sampling stations, presenting variations of about 9.3‰ for δ13C and 7.4‰ for δ15N. These results indicate that the isotopic values of species varied among the lakes, and that they are dependent on isotopic signals from phytoplankton.