The objective of this study was to evaluate the possible influential factors on the patterns of temporal distribution of testate amoebae (Protozoa: Arcellinida and Euglyphida) in plankton environments connected to a main river in a Neotropical floodplain. In this context, we hypothesised that the local factors would be the main structural factors for the testate amoebae. Samplings during two hydrological periods were conducted along a longitudinal axis of three environments for aquatic macrophytes, at the edge of the banks. The highest mean values of the richness, diversity and density were recorded for the high water period. Our results suggested that local factors influence the distribution of testate amoebae. These environments were significantly affected by the hydrological regime, where the main structural factors for testate amoebae were the environmental variables, supporting the predicted hypothesis.