A method for water resources protection based on spatial variability of vulnerability is proposed. The vulnerability of a water resource is defined as the risk that the resource will become contaminated if a pollutant is placed on the surface at one point as compared to another. A spatial modelling method is defined in this paper to estimate a travel time between any point of a catchment and a resource (river or well). This method is based on spatial analysis tools integrated in Geographical Information Systems (GIS). The method is illustrated by an application to an area of Massif Central (France) where three different types of flow appear: surface flow, shallow subsurface flow and permanent groundwater flow (baseflow). The proposed method gives results similar to classical methods of estimation of travel time. The contribution of GIS is to improve the mapping of vulnerability by taking the spatial variability of physical phenomena into account.