Traditional monitoring of lakes requires specialized personel and instrumentation for in situ and laboratory analysis. Continuous, up to date information is essential to all aspects of lake monitoring. The methodology presented here uses remote sensing technology, Geographical Information Systems (GIS) and hydrodynamic simulation for the study of lakes in West Mace-donia. Emphasis is given in Great Prespa lake, which is shared by Albania, Greece, and FYR of Macedonia in the Balkan Peninsula. An application of hydrodynamic simulation of Lake Vegoritis is also presented. The methodology provides information regarding lake’s surface water monitoring by extracting the circulation patterns that prevail in the lakes. Trends during the last 10 years of Great Prespa lake hydraulics, concerning internal distributions of temperatures, surface currents, circulation gyres, turbulence characteristics and transport phenomena are also identified. The methodology proved to be cost effective and has the potential to significantly improve the understanding and dynamical monitoring of lake hydraulics.