Groundwater resources in Morocco often face sustainability challenges due to increased exploitation and climate change. Specifically, the Al-Haouz-Mejjate groundwater in the Marrakesh region is faced with overexploitation and insufficient recharge. However, the complex subsurface geometries hamper hydrogeological modeling, characterization, and effective management. Reliably estimating aquifer substrate topography is critical for groundwater models but is challenged by limited direct measurements. This study develops nonlinear machine learning models to infer substrate depths by fusing sparse borehole logs with regional geospatial data. A Gaussian process regression approach provided robust holistic mapping, leveraging flexibility, and uncertainty quantification. Supplementary neural network architectures focus on isolating specific variable relationships, like surface elevation–substrate. Model accuracy exceeded 0.8 R-squared against validation boreholes. Spatial visualizations confirmed consistency across landscape transects. Elevation and piezometric data proved most predictive, though multivariate inputs were required for the lowest errors. The results highlight the power of statistical learning to extract meaningful patterns from disparate hydrological data. However, model opacity and the need for broader training datasets remain barriers. Overall, the work demonstrates advanced machine learning as a promising avenue for illuminating complex aquifer geometries essential for sustainability. Hybrid approaches that use both data-driven and physics-based methods can help solve long-standing problems with hydrogeological characterization.