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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 Arkeologjike i Shkodres (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. Palaeoenvironmental analysis of the two cores indicates that a wide marshland extended towards the present eastern coast of the lake, fed discontinuously both by surface- and ground-water, beginning sometime before 12,140 cal yrs BP. For about 7000 years ostracods do not record any significant changes, whereas the Characeae record in the proximal zone displays important variations. Those variations do not match any of the climatic oscillations revealed in previous studies by δ 18 O or pollen data, thereby implicating human activities. Ostracods and charophytes indicate that permanent shallow waters occurred in the Shkodra basin only around 5800 cal yrs BP. Historical sources of the Roman Empire indicate a swamp (the Palus labeatis ), crossed by the River Moraca, which flowed into the River Buna. Evidence for local fires, whether natural or anthropogenic, is recorded in SK13, scattered between 4400 and 1200 yrs BP. From 4400 to 2000 yrs BP, during the Bronze and Iron Age, hill forts ringed the marsh and burial mounds marked its edges. But around 2000 cal yrs BP, a dramatic change in the water body occurred: the disappearance of Characeae. Possibly fires were used for the elimination of natural vegetation and the subsequent cultivation of olive and walnut trees, causing an increase on organic matter input into the lake and thus, resulting on the disappearance of the Characeae due to higher turbidity in lake waters. This change occurred shortly after the arrival of the Romans. At 1200 cal yrs BP the marshland evolved into the large shallow lake we know today. This change is marked in the ostracod assemblages of both cores and agrees with trends in aquatic and riparian plants and may have allowed or encouraged exponential population growth beginning in the early-middle Medieval period and peaking in the late Medieval, as indicated in PASH settlement data. The use of different but complementary methods, drawn from palaeontology and archaeology, allowed reconstruction of Shkodra's past landscapes, linking the natural evolution of a Mediterranean lacustrine basin to regional population and settlement dynamics. This is the first research project to explore the relationship between natural and cultural landscapes and environmental change in northern Albania, forming the basis for further, more detailed studies.