In São Paulo State the crystalline aquifer system occupies an area of approximately 62,000 km² (~25% of the state area). Despite of low productivity and highly heterogeneous aquifer, the increasing water demand in the metropolitan areas has intensified crystalline aquifer exploitation. Typically, high productivity wells are related to thicker weathered profile and occurrence of expressive discontinuities, concentrating wellbore perforation along the lineaments as well as valley positions. However, many studies recognize poor relationship between well productivity and its geomorphological position suggesting other constraints control well productivity. Aiming to better understand the constraints and groundwater dynamics in crystalline aquifers, this work developed a numerical groundwater flow model to evaluate a conceptual model of a production well based on geological survey, structural data, electrical resistivity imaging, pumping test and stable isotope analysis. The study area encompasses a well field catchment located in the municipality of Itu (São Paulo, Brazil). The crystalline aquifer system is composed of phyllite and quartzite of the Neoproterozoic São Roque Group. The conceptual model assumes a set of subvertical discontinuities, responsible for a hydraulic connection between surface water and well, and four layers representing the weathered profile described in the study area. Constant head boundary conditions were associated to the rivers and reservoirs, which are connected to the well by a discrete feature representing the fracture sets. The model was calibrated by pumping test drawdown data providing hydraulic conductivity values from 1x10-9 m/s to 3.24x10-4 m/s. The numerical simulation estimated a production of 12.6% surface water after 1440 minutes of continuous pumping, corroborating the water mixture inferred from isotope analysis. The results show that recharge and well productivity are related to connectivity of crystalline aquifer with surface water, as well as the extent of the weathered zone. The constant renewal of groundwater and its interaction with surface water ensure the sustainable groundwater usage for the municipal water supply.