The delineation of well-head protection areas, especially for water supply wells, is of most importance in ensuring water quality. The areas delineated under this concept must be large enough to ensure that no pollutants will end-up and be pumped-off by abstraction wells but at the same time, small enough to minimize the social and economic cost of applying restriction measures to nearby land owners. The whole concept of applying well-head protection areas is based on the recognition of the hydrogeological parameters of the aquifer. The fact that these parameters are, by nature, characterized by uncertainty makes the whole application very difficult. In this paper, the delineation of well-head protection areas is simulated through a mathematical model and the methodology is applied on the aquifer of Moudania in Chalkidiki, taking into consideration a number of equally probable realizations of the geological structure of the aquifer. This aquifer is characterized by the spatial variability of its hydrogeological parameters, making the introduction of uncertainty in its simulation, an absolute necessity.