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Abstract The Guarani (GAS) and Serra Geral (SGAS) aquifer systems are the main groundwater sources in southern Brazil. We investigated the crucial relationship between the primary, intergranular pore system in the GAS and the secondary pore system associated with fractures in the SGAS in order to understand better the compartmentalization and connection, water storage, and productivity of both aquifers. Data from 375 wells that produce from both aquifers was used to evaluate the hydrodynamic characteristics of the GAS-SGAS contact. The integration of data using remote sensing, structural data, and thin section analysis support interpretations about the compartmentalization and potential connection of the aquifers. Fault zones trending NW, EW, and NNE demarcate six structural blocks in which the GAS-SGAS contact varies more than 400 m in elevation. Thin section analysis of sandstone texture and composition allowed us to determine the relationship between the type of porosity and cement type and content. The surface demarcating the Guarani-Serra Geral contact is highly productive in 93% of the wells that reach both aquifers. The integration of our results allowed us to propose a conceptual hydrogeological model for the GAS and SGAS aquifers in the study area.