Although the importance of long-term data has been emphasized by ecologists in recent years, little is known about how communities may change over time. In this study, we describe the general patterns of aquatic macrophyte diversity in the Paraná River floodplain observed during six years of study. Temporal changes in community composition were also evaluated. Data on the presence or absence of aquatic macrophytes were collected between March 2002 and March 2008, in six lakes associated with three rivers. Different analytical strategies were used to evaluate the dynamics of aquatic macrophyte communities between the different systems in the floodplain. The composition of aquatic macrophytes differed among the rivers, mainly with respect to the different vegetation life forms (floating, submersed, emergent and rooted with floating stems). The temporal similarity of species composition during the six years and the beta-diversity index indicated that the month-to-month species turnover was, in general, lower in the connected lakes, which are directly influenced by the river. Probably the water level fluctuation is a selective force that contributes to maintaining diversity or richness. Our findings indicated the importance of abiotic characteristics and connectivity of the lakes in determining macrophyte composition and community stability over a long time frame.