Understanding how small-scale differences in soil structure and chemistry affect the movement and reactions of water and dissolved substances underground is key to predicting environmental processes. We developed an approach that combines high-resolution imaging with advanced computer simulations to study these processes in detail. Using X-ray Computed Tomography (XCT), we map the 3D structure of pores in soil aggregates, while Scanning Electron Microscopy with Energy-Dispersive X-ray Spectroscopy (SEM-EDX) provides information on mineral composition at the same scale. These images are converted into models using the simulation platform OpenFOAM to analyze water flow, solute movement, and chemical reactions. The results show that features like flow channels, stagnant zones, and variations in mineral composition create localized “hotspots” where reactions occur more rapidly. We then use this information to improve larger-scale models of soil and groundwater systems. This integrated approach will help make predictions of water quality, nutrient cycling, and contaminant behavior more accurate and will eventually allow for the inclusion of microbial and multi-fluid processes.