The study of near‐pristine estuaries can be used as a tool for mitigation projects of harmful effects in anthropogenic eutrophic systems, since one can analyze the effect of temporal and spatial variations generated mainly by natural forces. Phytoplankton taxonomy has been used as a classical indicator to assess changes in transitional water communities, however alternative methods based on morphological, behavioral and physiological traits offer the opportunity to compare sites or moments with different taxonomic compositions. Our goal, in this context, is to evaluate phytoplankton community short‐term and seasonal variability in a near‐pristine estuary, Barra Grande estuary (Ilha Grande, RJ, Brazil), through species functional traits and thus community functional diversity. Samplings were carried out in a mooring in complete tidal cycles, seasonally during 2012. Our results showed a diverse phytoplankton community with 38 frequent and abundant taxa, marked by density variation (1.2 × 10.4–2 × 10.7 cell L−1) in depth, with abundance inversely related to tidal currents. The functional structure of the phytoplankton community measured by functional diversity (FD), varied seasonally in and across a gradient of tidal energy. A core community, mainly represented by flagellates and dinoflagellates, occurred in all observations and was highly functional (high FD), exploiting a variety of habitats. The chain‐forming diatoms were associated with high tidal energy, and occurred in higher densities during summer. Phytoplankton cell size, cell shape, and the ability to form colonies are extremely plastic traits that can be regulated by the environment, however, isolated tychopelagic diatoms were present in the study area across all seasons, with higher contributions in autumn and winter, reflecting the shallow characteristic of this system. During the winter, an exposed sandbar was formed, and the lack of connection with the ocean resulted in an abundance of riverine and brackish water taxa. In this near‐pristine estuary the densities and occurrences of HAB phytoplankton are low. Trait‐based analyses add information about community structure, which can be impacted by anthropogenic actions in urbanized coastal systems. Thus the information provided by this study regarding phytoplankton functional diversity and its relation to nutrients and hydrography in Barra Grande Estuary can be applied as a baseline model for the development of public policies.