Water infiltration from watersheds into the underlying groundwater aquifer systems of Northern Sacramento Valley is very important for the water resources in this area. An estimation of the runoff from the foothills region into the groundwater aquifer systems will contribute to better management of the aquifer to protect local water supply reliability and assist water managers in protecting water resources and ecosystems that are dependent on groundwater levels. The main objective of this study is to estimate the runoff from the foothills region into the groundwater aquifer systems around Butte County, California. In order to apply physically based distributed runoff models and estimate the runoff from watersheds precisely, reconstruction of historical atmospheric data at the fine spatial resolution which can be used as the input data to the models is important in the ungauged or sparsely gauged watersheds. In this study, Regional Hydro-Climate Model (RegHCM) was utilized for the dynamic downscaling of the historical global reanalysis atmospheric data (NCAR/NCEP) in order to reconstruct historical hydro-climate data over foothills region at the scale of 3 kilometers. The reconstructed data such as precipitation, air temperature and snow cover was validated based on the observation data or satellite driven data in time and space. The validation results are quite encouraging for the application of watershed hydrology models. Finally, the Watershed Environment and HYdrology (WEHY) model that utilizes upscaled hydrologic conservation equations to account for the effect of heterogeneity within natural watersheds was applied to the Sierra foothills region, encompassing Big Chico creek (192km2), Little Chico creek (78km2), Upper Butte creek (407km2) and Deer creek (508km2) watersheds in the northern California.