The Tijuana Estuary is a unique coastal plain and wetland-dominated estuary influenced by tidal fluctuations and saltwater inflow from the Pacific Ocean and by intermittent freshwater inflow from the Tijuana River. The lower Tijuana River valley, the alluvial river valley that leads into the estuary, collects 96% of runoff in the 4,500 km2 Tijuana River watershed. Stream flow in the Tijuana River is ephemeral and regulated by precipitation events and dam releases upstream in the watershed. The quality of surface water is impacted by sewage discharges in Mexico and storm water runoff. Groundwater in the river valley flows west to the estuary and is impacted by local agricultural and sod farming activities. The purpose of this study was to evaluate the influence of groundwater and surface water from the lower Tijuana River valley on salinity levels in the estuary and to characterize the interaction between surface water and groundwater in the estuary in response to diurnal tidal fluctuations. This study incorporated simultaneous monitoring of groundwater and surface water elevations and salinity in the lower Tijuana River valley and Tijuana Estuary over a period of 1.5 years. Seasonal variations in water levels and salinity were observed in the river valley and estuary; however, the estuary was influenced more by diurnal tidal fluctuations, high spring tides, major precipitation events, and surface water runoff. Groundwater and surface water salinity in the estuary was brackish to hypersaline. Hypersaline groundwater was measured in areas with low hydraulic conductivities that dictated slow infiltration rates and in areas that were inundated with ocean water during high spring tides. Hypersaline surface water was measured in estuarine channels that were temporarily disconnected to tidal flushing. Precipitation events dramatically affected salinity in surface water where salinity temporarily fell below brackish levels. In groundwater, precipitation events typically caused a short-term spike in salinity as the initial wetting front of infiltrating rainwater carried a higher concentration of dissolved salts from the shallow soil to the water table. Continued recharge by infiltrating rainwater gradually decreased salinity over a few days after the precipitation event. These observations demonstrated that the Tijuana Estuary is a highly variable and dynamic environment that is greatly influenced by diurnal tidal fluctuations, particularly during high spring tides, and major precipitation events and subsequent storm water runoff. It appeared that seasonal variations observed in the lower Tijuana River valley did not influence the hydrologic nature of the estuary. The CD-ROM, an appendix to the thesis, is available for viewing at the Media Center of Love Library.