Fine-grained sedimentary rocks such as shale or mudstone are ubiquitous in sedimentary basins and play important roles as caprocks, host rocks, or source rocks in many energy technologies including carbon capture and storage, nuclear waste storage, and hydrocarbon extraction. Fine-grained soils are equally ubiquitous and play important roles in soil carbon storage and food security. Accurate predictive models of the hydrologic properties of these media remain elusive, however, because of the significant experimental challenges posed by their low mechanical strength, ultra-low permeability, and sensitivity to geochemical and geomechanical alteration. An even greater challenge is that nanoscale interactions between clay particles give rise to strong couplings between the chemistry, mechanics, and hydrology of these media. Our research aims to gain fundamental insight into these interactions and couplings by using computational fluid dynamics, discrete element model, brownian dynamics, and atomistic-level simulations of water-clay-salt-(organic) systems.