Amazonian aquatic environments are complex, and their interaction promotes heterogeneous environments that turn difficult the development of patterns to describe them. We evaluated if interannual variation in the physical-chemical structure and the phytoplankton community promote environmental and biological contrasted conditions between similar hydrological periods. Amazonian floodplain lakes have different environmental and biological responses in similar water periods due to the interannual variation. Phytoplankton community structure has differences between periods, but these differences do not necessary promote dissimilarities. Most of the phytoplankton species belong to the same functional groups. The composition of species and functional groups between sample units inside lakes is variable and may have or not significant differences in dissimilarity, but both periods are equally heterogeneous. Beta diversity has shown that the replacement of species and functional groups causes a great level of variation between sites, which maintain a high heterogeneity between periods. These variations have different responses for different scales turning a difficult task the interpretation of patterns for these environments. Hence, scale and interannual variability are factors that need to be carefully considered when setting standards to describe the ecological dynamics of floodplain lakes in the Amazonian system.