We present the first insight to the oceanography of the southeastern Adriatic Sea, where coastal water influenced by Albanian rivers comes into contact with the inflowing oligotrophic Eastern Adriatic Current (Ionian Surface Water and Levantine Intermediate Water). A distinct plankton distribution was observed on each side of the shelf break hydrographic boundary in May 2009, during gradual warming of the surface waters. The prochlorophytes accumulated along the nutricline above the shelf and continental slope. The phosphorus limited inshore waters were dominated by a small diatom Chaetoceros circinalis, dinoflagellates, cryptophytes, autotrophic picoplankton, and heterotrophic nanoplankton. The offshore surface layer was characterized by bigger nanoplankton (coccolithophorids, green flagellates). Low nutrient concentrations influence relatively low productivity not only above the Albanian shelf but also further to the north along the Montenegrine and Croatian coastal Adriatic Sea.