The estimation of groundwater recharge and its spatial and temporal variability in a drainage basin is essential for sustainability assessments and requires, in most cases, the use of an appropriate 3D numerical flow and transport model. For most drainage basins, the bedrock and overburden geology maps exist, the location and geometry of major structural features can be identified using available GIS databases, and surface water and terrain elevation data at an appropriate scale are readily available. In order to use 3D models to provide an initial assessment of the sustainability of the groundwater resource extraction of a specific drainage basin, the 3D model has to be populated with hydraulic properties that are consistent with the range of values that are representative of the rock types that underlie the drainage basin. A review of hydrogeological data from a number of sites shows that while there is a wide range in the hydraulic properties of fractured rocks in general, the range for individual rock types is more constrained, (i.e. fractured granite versus fractured gabbro). There is a great amount of hydrogeological data from fractured rock masses that have been investigated in detail as part of nuclear waste, mining and civil engineering projects around the world. Data from a specific site can be used as a first approach in another one, not investigated, once they have the same geologic characteristics and tectonic environment. This approach was used to model the sustainable groundwater yield of a small drainage basin in Southeast Brazil. Data on major structures and fracture systems were extracted from satellite images, aerial photos and outcrop expositions using GIS environment. The groundwater flow model was constructed using terrain elevation data, geology maps, hydrological records, as well as soil type and land use maps. FEFLOW (Diersch, 1988) was used to simulate the spatial and temporal distribution of groundwater recharge in the basin, using different pumping scenarios. The model was capable to yield a good estimation of groundwater resources in the watershed, as a first approach, and to assess groundwater and surface water relations in natural conditions and in stress scenarios being a useful tool for sustainability analysis of groundwater exploitation.