This study of alluvial aquifer basins in southern California is centered on observations of differential surface displacement and the search for the mechanisms of deformation. The San Bernardino basin and the Upper Coachella Valley aquifers are bound by range fronts and fault segments of the southern San Andreas fault system. I have worked to quantify long-term compaction in these groundwater dependent population centers with a unique synthesis of data and methodologies using Interferometric Synthetic Aperture Radar (InSAR) and groundwater data. My dissertation contributes to the understanding of alluvial aquifer heterogeneity and partitioning. I model hydrogeologic and tectonic interpretations of deformation where decades of overdraft conditions and ongoing aquifer development contribute to extreme rapid subsidence. I develop the Hydrogeologic InSAR Integration (HII) method for the characterization of surface deformation in aquifer basins. The method allows for the separation of superimposed hydraulic and/or tectonic processes in operation. This formalization of InSAR and groundwater level integration provides opportunities for application in other aquifer basins where overdraft conditions may be causing permanent loss of aquifer storage capacity through compaction. Sixteen years of SAR data for the Upper Coachella Valley exhibit rapid vertical surface displacement (#8804; 48mm/a) in sharply bound areas of the western basin margin. Using well driller logs, I categorize a generalized facies analysis of the western basin margin, describing heterogeneity of the aquifer. This allowed for assessment of the relationships between observed surface deformation and sub-surface material properties. Providing the setting and context for the hydrogeologic evolution of California's primary aquifers, the mature San Andreas transform fault is studied extensively by a broad range of geoscientists. I present a compilation of observations of creep, line integrals across the Pacific-North America Plate Boundary, and strain tensor volumes for comparison to the Working Group 2007 (UCERF 2) seismicity-based deformation model. I find that the moment accumulation across the plate boundary is consistent with the deformation model, suggesting fault displacement observations within the plate boundary zone accurately capture the strain across the plate boundary. This dissertation includes co-authored materials previously published, and also includes unpublished work currently under revisions for submission to a technical journal.