With the aim of determining space-time distribution of zooplankton related to the hydrochemistry in the Vitoria Bay estuarine system (south-eastern Brazil), samples were collected at ten sampling stations using a 200 micron mesh size plankton net. Non-biotic parameters including salinity, temperature, dissolved oxygen, alkalinity and pH, as well as chlorophyll-a and dissolved nutrients (N-NO3-, N-NO2-, N-NH4+, TDN, P-PO43- and H4SiO4) were studied. The estuary was characterized by two distinct regions in relation to the distribution of the hydrochemical parameters: an inner region under the influence of the continental water input, characterized by high nutrient concentration and temperature, and an outer region where the influence of coastal waters predominated with high salinity, alkalinity and dissolved oxygen values. Nutrient concentrations (N and P) were high mainly during the dry period, indicating a possible eutrophication state of the system. Copepoda dominated the zooplankton community with Acartia lilljeborgi Giesbrecht, 1892, Acartia tonsa Dana, 1848, Temora turbinata (Dana, 1849), Bestiolina sp (Sewell, 1912), Oithona hebes Giesbrechti, 1891, Oithona oculata Farran, 1913, Paracalanus quasimodo Bowman, 1971 and Parvocalanus crassirostris Dahl, 1894 being the most abundant species. Highest abundances occurred during summer and lowest in spring. The zooplankton community showed a seasonal distribution pattern where Acartia lilljeborgi and A. tonsa were more abundant in summer and winter, and copepodites of Pseudodiaptomus spp in spring. Regarding the spatial component, canonical correspondence analysis (CCA) revealed that the outer region of the estuary was characterized by estuarine and coastal species (e.g. Acartia lilljeborgi) and the inner region by the typical inner estuary species (e.g. Pseudodiaptomus richardi Dahl, 1894). The maintenance of this spatial pattern was influenced mainly by the interaction of coastal waters with the continental water input, since this interaction produced a horizontal gradient of salinity in the estuary, delimiting the two regions and, consequently, the distribution of the species.