Phytoplankton distribution and environmental characteristics were determined in a shallow, highly stratified and oligotrophic estuary (Zrmanja, eastern Adriatic). Samples were collected in two contrasting seasons; winter (February 2000), when river discharge was high, and in summer (July 2003), a period of drought. Phytoplankton distribution was closely related to salinity gradients, nutrient levels, and water residence time. Microscopic analysis revealed that phytoplankton was composed mainly of marine diatoms, dinoflagellates, cryptophytes, green flagellates, and coccolithophorids. The dominant biomarker pigments were fucoxanthin, alloxanthin and 19'-hexanoyloxyfucoxanthin, while lower, but indicative contributions of peridinin and chlorophyll b were also noted. Maximum abundance and biomass were found in the middle estuary in winter and in the upper estuary in summer. The estuary is mostly P-limited. Development of chain-forming marine diatoms was evident in winter. Due to the reduced nutrient input in summer, the biomass accumulated in the upper estuary (1,000 ng chlorophyll a l⁻¹) was composed mostly of nanoplanktonic unicellular diatoms, nanoplanktonic marine dinoflagellates, cryptophytes, and chlorophytes. The concentrations of about 200 ng l⁻¹ hex-fuco, suggested that the contribution of prymnesiophytes to total biomass was comparable to that of diatoms and dinoflagellates. In the middle estuary and coastal sea, PO₄ and TIN were 3.5 times lower, resulting in a fivefold decrease in biomass (<100 ng chlorophyll a l⁻¹). The oligotrophic Zrmanja and other karstic rivers discharging in the eastern Adriatic Sea, provide insufficient source of nutrients and low productivity of the eastern Adriatic Sea.