The roles of graphene oxide (GO) particle geometry, GO surface orientation, surface roughness, and nanoscale chemical heterogeneity on interaction energies, aggregation, retention, and release of GO in porous media were not fully considered in previous studies. Consequently, mechanisms controlling the environmental fate of GO were incompletely or inaccurately quantified. To overcome this limitation, plate-plate interaction energies were modified to account for these factors and used in conjunction with a mathematical model to interpret the results of GO aggregation, retention, and release studies. Calculations revealed that these factors had a large influence on the predicted interaction energy parameters. Similar to previous literature, the secondary minimum was predicted to dominate on smooth, chemically homogeneous surfaces that were oriented parallel to each other, especially at higher ionic strength (IS). Conversely, shallow primary minimum interactions were sometimes predicted to occur on surfaces with nanoscale roughness and chemical heterogeneity due to adsorbed Ca2+ ions, especially when the GO particles were oriented perpendicular to the interacting surface. Experimental results were generally consistent with these predictions and indicated that the primary minimum played a major role in GO retention and the secondary minimum contributed to GO release with IS reduction. Cation exchange (Na+ replacing Ca2+) enhanced GO release with IS reduction when particles were initially deposited in the presence of Ca2+ ions. However, retained GO were always completely recovered into the excess deionized water when the sand pore structure was destroyed during excavation, and this indicates that primary minima were shallow and that the pore structure also played an important role in GO retention. Further evidence for the role of pore structure on GO retention was obtained by conducting experiments in finer textured sand and at higher input concentrations that induced greater aggregation. In both cases, greater GO retention occurred, and retention profiles became more hyperexponential in shape.