Phytoplankton assemblages were studied to characterize the trophic status of the semienclosed Vlora Bay (Albania) and to evaluate the influence of terrestrial inputs on its pelagic ecosystem. The study was carried out as part of the European Project CISM (INTERREG IIIA Italy–Albania) and conducted during two oceanographic cruises (spring 2007, winter 2008). The size-fractionated chlorophyll a concentrations, primary production rates, and the chemotaxonomic composition (high-performance liquid chromatography) of the phytoplankton assemblages were measured. The spatial variability of primary production rates and chlorophyll a concentrations both showed a pronounced E-W gradient in the surface layer, with the highest values along the eastern coast. In spring, a deep chlorophyll maximum was observed in the central western part of the bay, whereas in winter a homogeneous vertical distribution was observed. The phytoplankton assemblages were quite similar in both seasons and were dominated by the picophytoplankton fraction (≈46% and 53% in spring and in winter, respectively). Haptophytes and pelagophytes were the major phytoplankton groups, and accounted, respectively, for 50% and 15% in spring, and 40% and 25% in winter. The results showed that Vlora Bay was characterized by generally oligotrophic conditions and that the influence of the southern Adriatic open waters was negligible. The trophic characteristics of the pelagic ecosystem of the bay were essentially driven by terrestrial inputs.