In 2014 the SWAT (Soil and Water Assessment Tool) model was used as a basis for follow-up investigations of Moldova's small rivers potential flow. The first step of the study included the validation of SWAT for local conditions. As an experimental area, the Cogilnic River watershed was selected. Interim steps included the watershed delineation aimed to identify the subwatersheds and the Hydrological Response Units (small entities with the same characteristics of hydrologic soil type, land use and slopes). To address these tasks, the land cover, soil and slope layers, based on the Digital Elevation Model, were integrated in the SWAT environment. These thematic layers, alongside with long-term information on local monthly maximum and minimum temperatures and precipitation, enabled reflecting the differences in hydrological conditions and defining the watershed runoff. However, the validation of the modelling outputs, carried out through comparison of a simulated water yield from the studied watershed with actual Cogilnic streamflow measures, observed in 2010-2012, showed a great discrepancy between these parameters caused by anthropogenic loading on this small river. Thus, a 'classical' SWAT modelling needs to account for real environmental conditions and water use in the study area.