Watershed Dynamics in the Prespa Lakes: An Integrated Assessment of Stream Inflow Effects

The Prespa Lakes system, shared between Greece, the Republic of North Macedonia, and Albania, forms a significant transboundary, large-scale integrated freshwater ecosystem subject to multiple anthropogenic and natural pressures. This study focuses on the Greek part of the Prespa Lakes system with particular emphasis on the identification of the ecological and hydrological impacts of the contributing stream inflows on the lakes by examining the spatial variability in physicochemical and biological conditions and conducting water balance and isotopic analyses. Based on our results, streams draining into Lesser Prespa Lake exhibited more pronounced hydrological and physicochemical fluctuations than the Agios Germanos River connected to Great Prespa Lake, while ecological status classifications of all studied streams ranged from high to moderate. Furthermore, moderate ecological status conditions (mainly observed at the downstream stations) were closely associated with adjacent anthropogenic pressures, including agricultural drainage, livestock activities, irrigated croplands, and wastewater discharges. In addition, although both lakes were classified as mesotrophic, field data indicated greater transparency loss in Lesser Prespa than in Great Prespa Lake. Regarding the stream influences on Lesser Prespa Lake’s water quality, nutrient loads induced changes in lake concentrations by roughly one month. Total nitrogen showed moderate stream–lake correlations (R = 0.61) and a strong negative correlation for total phosphorus (R = −0.94), suggesting substantial nutrient retention and processes within the lake. Water balance analysis revealed an annual water deficit for both Lesser and Great Prespa, with the latter exhibiting a markedly stronger and systematic long-term decline in water level. In the Lesser Prespa, seasonal fluctuations in water volume were primarily driven by excess rainfall, while stream inflows contributed minimally. Conversely, correlation analysis for Great Prespa identified surface inflow from the Ag. Germanos catchment as the dominant driver of water storage variability, surpassing direct rainfall, with strong correlations in both wet (R = 0.79) and dry (R = 0.88) periods. Isotopic compositions (δ18O, δ2H) did not differ significantly between the two lakes, indicating common recharge sources and strong evaporative imprints, while stream isotopic signatures highlighted spatial and seasonal variability in hydrological inputs. Seasonal and spatial variations were proved to be strongly influenced by both natural hydrological dynamics and anthropogenic pressures within the basin, while these findings reinforce the importance and the necessity of adopting holistic, cross-border management strategies that maintain the ecological integrity and the long-term sustainability of the Prespa Lakes ecosystem.