The horizontal distribution of plankton communities in a subtropical mixed estuarine system over one tidal cycle was investigated. Hydrological and planktonic samples were obtained twice on 17 July 2007 in a transect with ten stations in the Babitonga Bay estuary, south Brazil (~26°S). Hydrological variables did not vary spatially or tidally during samplings. However, in the cluster analyses both phyto and zooplankton were structured according to their estuarine position and in the inner stations also by the tidal condition. Phytoplankton abundances were higher during fl ood tide in the inner estuary (max. 122,583 ind.L -1 ), where diatoms dominated, particularly Diploneis bombus. However, the density at ebb tide increased towards outer estuary (max. >100,000 ind.L -1 ) and fl agellates, mostly Gymnodinium spp., became abundant.Zooplankton abundances were higher at intermediate stations during both tides (max.13,691 ind.m -3 ). The innermost stations were dominated by the copepod Acartia tonsa, while in the outermost stations Temora turbinata and the polychaete larvae Loimia sp. dominated. The results demonstrate how variable the estuarine plankton horizontal structure can be over short time-scales even in mixed estuarine systems under relatively homogeneous conditions, highlighting the importance to consider such temporal scales for a more accurate understanding of the dynamics of these communities.