An increase in abundance of potentially toxic dinoflagellates in the Santos channel, located in a highly urbanized and eutrophic estuarine complex, was reported in the literature. Prediction of such occurences is essential, but phytoplankton community structure in dynamic estuarine systems are difficult to analyze. In the present work, we attempted to discuss microphytoplanktonic community in relation to physical variables looking for shifts in composition, in time scales of 25 hours. To achieve our goal two surveys were performed on anchored stations during 25 hours (two complete tidal cicles) in the Santos channel, during November 2005 and March/April 2006. Diatom community enhanced in periods of lower current velocity (tide peaks) during dry season, probably due to lower stratification after tidal runs and light availability, while dinoflagellates enhanced after rainfall events, probably due to a higher haline stratification and an increase in dissolved nutrients. The occurrence in high density of Pseudo-nitzschia "seriata" and Prorocentrum minimum reinforces the necessity of a constant monitoring program in the region.