Mass transport can have a significant effect on chemical diagenetic processes in sedimentary basins. This paper presents results from the first part of a study that was designed to explore the role of an evolving hydrodynamic system in driving mass transport and chemical diagenesis, using the San Joaquin basin of California as a field area. We use coupled hydrogeologic models to establish the paleohydrogeology, thermal history, and behavior of nonreactive solutes in the basin. These models rely on extensive geological information and account for variable-density fluid flow, heat transport, solute transport, tectonic uplift, sediment compaction, and clay dehydration.