The alpha, beta, and gamma diversity are important tools for conservation studies, and the distribution of species in space and time is essential to provided insights regarding diversity patterns and processes that modify the ecosystem and the community responses to such changes. Thus, a long-term ecological date was used to evaluate in 12 biotopes the phytoplankton composition and diversity within selected habitats (alpha diversity), between habitats (beta diversity) and across the upper Paraná River floodplain (gamma diversity). We evaluate the environmental variability of the hydrosedimentological cycles (limnophase and potamophase) during 12 years, associated with the water level variability and with the environmental heterogeneity as drivers of the phytoplankton composition and diversity in the upper Paraná River floodplain. Remarkable gamma diversity was recorded especially in limnophase, however, years with intense flood presented high gamma diversity, and years with extreme drought presented low gamma diversity, although without significant differences. The alpha diversity was significantly different on spatial and temporal scales. The beta diversity showed high values, however with low temporal variability and without correlation with the hydrosedimentological regime of the Paraná River. Overall, these results indicate that the variability in the hydrosedimentological regime associated with the periodicity, duration, and amplitude of limnophase and potamophase, and the pattern of mosaic of habitats in this floodplain are essential for sustaining much of the diversity phytoplankton diversity and ecosystem integrity, and that this approach is relevant and proved be useful to understand floodplain systems and associated phytoplankton community.