It is not possible, using numerical methods, to model groundwater flow and transport in the fractured crystalline rock of northeastern Brazil. As an alternative, the usefulness of self-organizing map (SOM), k-means clustering, and Davies-Bouldin techniques to conceptualize the hydrogeology was evaluated. Also estimated was the well yield and groundwater quality across the Juá region. This process relies on relations in the underlying multivariate density function associated with a sparse local set of hydrogeologic (electrical conductivity, geology, temperature, and well yield) and a complete regional set of airborne geophysical (electromagnetic, magnetic, and radiometric) and satellite spectrometric measurements. Resampling of the regional well yield and electrical conductivity estimates provides sufficient resolution to construct variograms for stochastic modeling of the hydrogeologic variables. The combination of these stochastic maps provides a way to identify potential drilling targets for future groundwater development. The data-driven estimation approach, when applied to available airborne electromagnetic and water-well hydrogeologic measurements, provides a low-cost alternative to numerical groundwater flow modeling. In addition to fractured rock environments, the alternative modeling framework can provide spatial parameter estimates and associated variograms for constraints to improve the traditional calibration of equivalent groundwater-porous-media models.