Temporal stability in beta diversity does not guarantee surrogacy or compositional stability in a micro-phytoplankton meta¬community. In this study, we evaluated phytoplankton community organization (i.e., microalgae filtered in 20 μm mesh-sized plankton net) in a highly dynamic subtropical tidal river over three years. Specifically, we assessed temporal stability in the spatial organization of phytoplankton, the diatoms’ efficiency as an indicator (surrogate group) of ecological patterns of other phytoplankton groups, the temporal variation in species composition, and the beta diversity of a metacommunity. We performed six sampling occasions at the end of the summers and winters from 2017 to 2019 at 16 sampling points comprising a strong en¬vironmental gradient in the Guaraguaçu River, South Brazil. We tested for correlations of community structures from different periods and for correlations between diatoms species and those from other phytoplankton groups using Mantel tests. Species compositions were compared among periods using a permutational multivariate analysis of variance, and temporal variation in metacommunity beta diversity was evaluated using null models. There was temporal stability in the spatial dissimilarities of communities. Diatoms were poorly correlated with the other phytoplankton groups. The temporal stability in spatial structure, a facet of beta diversity, was in line with the temporal stability in compositional variation – a measurement of metacommuni¬ty beta diversity. Our results also showed that such stability was not static, since community compositions varied over time, mainly between seasons. We conclude that even in a highly dynamic tidal river, the temporal stability of spatial organization may indicate that the spatial gradient is so strong that it maintains spatial structuring over time. Such patterns were maintained even with the dynamic species changes over seasons. The fact that different phytoplankton groups do not respond similarly to the spatial gradient reinforces that microalgae should be analyzed separately in ecological studies, and long-term monitoring should consider different algal groups for a complete assessment of ecological patterns.