Development of the coastal aquifer systems of Southern California has resulted in overdraft, changes in streamflow, seawater intrusion, land subsidence, increased vertical flow between aquifers, and a redirection of regional flow toward pumping centers. These water-management challenges can be more effectively addressed by incorporating new understanding of the geologic, hydrologic, and geochemical setting of these aquifers.

Groundwater and surface-water flow are controlled, in part, by the geologic setting. The physiographic province and related tectonic fabric control the relation between the direction of geomorphic features and the flow of water. Geologic structures such as faults and folding also control the direction of flow and connectivity of groundwater flow. The layering of sediments and their structural association can also influence pathways of groundwater flow and seawater intrusion. Submarine canyons control the shortest potential flow paths that can result in seawater intrusion. The location and extent of offshore outcrops can also affect the flow of groundwater and the potential for seawater intrusion and land subsidence in coastal aquifer systems.

As coastal aquifer systems are developed, the source and movement of ground-water and surface-water resources change. In particular, groundwater flow is affected by the relative contributions of different types of inflows and outflows, such as pump-age from multi-aquifer wells within basal or upper coarse-grained units, streamflow infiltration, and artificial recharge. These natural and anthropogenic inflows and outflows represent the supply and demand components of the water budgets of ground-water within coastal watersheds. They are all significantly controlled by climate variability related to major climate cycles, such as the El Niño–Southern Oscillation and the Pacific Decadal Oscillation. The combination of natural forcings and anthropogenic stresses redirects the flow of groundwater and either mitigates or exacerbates the potential adverse effects of resource development, such as declining water levels, sea-water intrusion, land subsidence, and mixing of different waters. Streamflow also has been affected by development of coastal aquifer systems and related conjunctive use.

Saline water is the largest water-quality problem in Southern California coastal aquifer systems. Seawater intrusion is a significant source of saline water, but saline water is also known to come from other sources and processes. Seawater intrusion is typically restricted to the coarse-grained units at the base of fining-upward sequences of terrestrial deposits, and at the top of coarsening upward sequences of marine deposits. This results in layered and narrow intrusion fronts.

Maintaining the sustainability of Southern California coastal aquifers requires joint management of surface water and groundwater (conjunctive use). This requires new data collection and analyses (including research drilling, modern geohydrologic investigations, and development of detailed computer groundwater models that simulate the supply and demand components separately), implementation of new facilities (including spreading and injection facilities for artificial recharge), and establishment of new institutions and policies that help to sustain the water resources and better manage regional development.