Freshwater inflows are a crucial component for maintaining estuarine health, function and productivity. Streamflows, the primary source of freshwater inflows, have been modified and altered from their natural flow by population growth and anthropogenic impacts on the contributing watersheds. The Guadalupe Estuary is a primary habitat for many endangered species. The Guadalupe River Watershed, which supplies 70% of freshwater inflows, experiences rapid urbanization and agricultural development. This study proposed to characterize the impact of land use/cover change in the Guadalupe River Watershed on freshwater inflows to the Guadalupe Estuary. Pre-whitening, Mann-Kendall and bootstrap techniques were used to test for significant trends on streamflow and precipitation. Analyses suggested more trends in annual and seasonal minimum and mean streamflow than would be expected to occur by chance in the periods of 1930-2005 and 1950-2005. No significant trends were found in the period of 1970-2005. Significant trends were more prominent in the upper watershed and decreased as analysis moved downstream in the period of 1950-2005. Trend tests on precipitation data in the period of 1950-2005 revealed more significant trends than would be expected by chance in mean annual and winter precipitation. Analyses of Landsat images of the watershed using an unsupervised classification method showed an increase in forest, urban and irrigated land by 13, 42 and 7%, respectively, from 1987 to 2002. Urbanized areas were mostly found in the middle part of watershed surrounding the I-35 corridor. More than 80% of irrigated lands are distributed over the San Marcos and Middle Guadalupe River Watersheds. Soil and Water Assessment Tool (SWAT) model was applied for the Guadalupe River Watershed. Calibration and validation using data recorded at USGS 08176500 indicated the model performed well to simulate streamflow. The coefficient of Nash- Sutcliffe, determination and percent bias were 0.83, 0.96 and 3.81, respectively, for calibration and 0.68, 0.75 and 29.38 for validation period. SWAT predicted a 2% decrease in annual freshwater inflow rates from the effect of land use/cover change from 1987 to 2002. Reservoirs increased freshwater inflows during low flow months and decreased the inflows during high flow months. Precipitation variability changed characteristics of monthly freshwater inflows.