The Micro Prespa basin is a trilateral catchment area of significant importance with a unique ecosystem closely related to the homonymous lake. In this frame, a fully operational monitoring project was carried out including continuous real-time measurements in Micro Prespa Lake with the use of a multi-sensor probe, as well as periodical sampling and analyses of all available water systems for an extended set of 85 parameters. Four main interacting water systems were identified, including alluvial and karstic aquifers, Micro Prespa Lake and adjacent drainage network. The results outlined that general environmental conditions are satisfying in respect to the relative legislation and the hydrogeochemical signatures. However, trends of environmental pressures were ascertained as a result of natural (geogenic) factors, embracing seasonal peaks for Ni, Pb, and NH4 mainly in groundwater systems. Based on chlorophyll a records, Micro Prespa is classified as oligotrophic to slightly mesotrophic, subjected to seasonal variations. Heavy metal concentrations are low, except Ni which appears to have elevated values during the dry hydrological period. Finally, the hydrogeochemistry of drainage network is primarily influenced by surface runoff of the surrounding mountainous areas, hence elevated phosphorus values of the Aghios Germanos stream are possibly linked with the leaching of the granitic formations on the east.