Abundance and structure of phytoplankton and zooplankton, along with their relationship to hydrographic conditions were determined in the highly stratified estuary of the karstic Ombla River, south-eastern Adriatic. Sampling was carried out during 17 cruises within a one year period. River discharge lowered surface salinity and enriched the estuary with NO3 and SiO4. Nutrient ratios suggested that PO4 was the most likely limiting nutrient for phytoplankton growth in the estuary. Diatoms were present in low numbers and dominated the winter–early spring period. Dinoflagellates dominated from the end of May to August. Phytoplankton and zooplankton were composed mostly of marine species and their abundance decreased in seaward direction. Planktonic populations are controlled by the river runoff, temperature, salinity, nutrient concentrations and grazing. The results were consistent with the hypothesis that no algal blooms have been recorded due to short renewal time.