A multidisciplinary micro-paleontological study of a sediment core (SK19) drilled in the coastal area of Lake Shkodra, northern Albania, integrated with archaeological data from the Projekti Arkeologjikë i Shkodrës (PASH), provides compelling evidence for a long-term relationship between Shkodra's natural environment and its inhabitants. Charophyte and ostracod data recovered from SK19 combined with those already studied from the distal core SK13 (Mazzini et al., 2015), reveal important information concerning the changing characteristics of the water body through time. In particular, the ostracod fauna display a truly Balkanic character with eight taxa endemic to the area.