Daily fluctuation of rotifer population abundance was studied in a lake and in a river of the Upper Paraná River floodplain. Samples were collected in the open water for 14 consecutive days, in the high and low water periods. Densities were higher in the lake, chiefly in the low water period. During the studied period, changes in species dominance were observed. Rotifer abundance showed that higher variability occurred during the high water period in both environments. Rotifer abundance showed high variability in the river during the sampling days. In the lake, fluctuation was related to the hydrological periods. Rotifer abundance fluctuations in the lake were influenced by regional factors (fluviometric level); and in the river by local factors (flow). The sampling design pointed out that seasonal samples are necessary to evaluate rotifer abundance in the lake. However, this is not the case in the river where seasonal differences in abundance were not observed