An increase in abundance of potentially toxic dinoflagellates in Santos channel, located in a highly urbanized and eutrophized estuarine complex, was reported in 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 to looking for shifts in composition in time scales of 24 hours and in pluviometric extremes. To achive our goal two surveys were performed on anchored stations of 25 hours (two complete tidal cicles) in Santos channel, during November 2005 (“dry season”) and April 2006 (“rainy season”). Diatoms 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 occurance of Pseudo-Nitzschia spp and Prorocentrum minimum blooms reinforces the necessity of a constatnt monitoring program in the region.