The intrinsic vulnerability of a karstic aquifer system in central Greece was jointly assessed with the use of a statistical approach and PI method, as a function of topography, protective cover effectiveness and the degree to which this cover is bypassed due to flow conditions. The input data for the index-overlay PI method were derived from field works and 71 boreholes of the area; the information was obtained, subsequently its critical factors were compiled which included lithology, fissuring and karstification of bedrock, soil characteristics, hydrology, hydrogeology, topography and vegetation. The aforementioned parameters were processed jointly with the aid of a GIS and yielded the final estimation of intrinsic aquifer vulnerability to contamination. Results were compared with an equivalent spatially distributed probability map obtained through a stochastic approach. The calibration and test phase of the latter relied on morphometric conditions derived by terrain analyses of a digital elevation model as well as on geology and land use from thematic maps. This procedure allowed taking into account the topographic influences with respect to a deep system such as the local karstic aquifer of eastern Kopaida basin. Finally, results were validated with ground truth nitrate values obtained from 41 groundwater samples, highlighted the spatial delineation of susceptible areas to contamination in both cases and provided a robust tool for regional planning actions and water resources management schemes.