This chapter provides physical settings, particularities and other abiotic aspects in the broadest sense, focusing specifically on natural lake ecosystems. Being located at the southwestern part of the Balkan Peninsula and influenced by Mediterranean and continental climate the large Balkan Lakes of Prespa, Ohrid and Skadar/Shkodra are at the crossroad of accelerated climate implications. Lakes and their water ecosystems, both of natural or anthropogenic origin, dominate in the Albanian mosaic landscape and contributing to the high diversity of habitats and species as well as environmental heterogeneity. Albania has abundant water resources because to its climate, particularly its high rainfall and mountainous mountain relief. A significant volume of water from other nations drains through Albania since the topographical drainage system does not match the Albanian border with its neighbors. The entire area of wetlands is 970 km2, or roughly 3% of the country’s total land area. The majority of these aquatic environments are made up of lakes, coastal lagoons, and reservoirs. All of these include a high diversity of habitats and species, sensitive ecosystems that are still heavily impacted by human activity and are not well studied. Unquestionably, the three large transboundary lakes of Ohrid, Prespa, and Shkodra are the most significant aquatic complexes for Albania and the entire Balkan region. Their combined area, including the Drini watershed, is 19,352 km2, of which 257 km2 are in Greece, 3583 km2 in North Macedonia, 4152 km2 in Montenegro, 4360 km2 in Kosovo, and 7000 km2 are in Albania. From Prespa Lake to the Adriatic Sea’s Buna delta, they form a cascade system.