Urban areas are typically characterized by the presence of industrial sites, which are often sources of groundwater contamination, posing a serious threat for the groundwater. In such cases, a crucial step is to find a link between the contaminant sources and freshwater supply wells at risk. As a part of the AMIIGA Project, two different stochastic approaches were applied to assess drinking water supply wells vulnerability in Functional Urban Areas in the presence of several chlorinated hydrocarbons sources in an alluvial aquifer in Milano and a pesticide mega site in a complex geological setting in Poland. In the first case study, the innovative Pilot Point Null-Space Monte Carlo forward particle tracking was used, applying a forward solution instead of the classical backtracking, while in the second case was chosen the classical Monte Carlo methodology. Both case studies represent useful application examples, allowing an effective prioritization of expensive remediation actions in order to protect freshwater wells.