Karst aquifers vulnerability assessment and mapping are important tools for improved sustainable management and protection of karst groundwater resources. In this paper, in order to estimate the vulnerability degree of the karst aquifer feeding the Pertuso Spring in Central Italy, COP method has been applied starting from two different discretization approaches: using a polygonal layer and the Finite Square Elements (FSE). Therefore, the hydrogeological catchment basin has been divided into 72 polygons, related to the outcropping lithology and the karst features. COP method has been applied to a single layer composed by all these polygons. The results of this study highlight vulnerability degrees ranging from low to very high. The maximum vulnerability degree is due to karst features responsible of high recharge and high hydraulic conductivity. Comparing the vulnerability maps obtained by both methodologies it is possible to say that the traditional discretization approach seems to overestimate the vulnerability of the karst aquifer feeding the Pertuso Spring. Between the two different approaches of COP method, the proposed polygonal discretization of the hydrogeological basin seems to be more suitable to small areas, such as the Pertuso Spring hydrogeological basin, than the traditional grid mapping.