Methods are developed to study hydrologic interactions across the surficial/groundwater interface in a native prairie ecosystem. Surficial ecohydrologic processes are simulated with the USDA's EPIC model using daily climate data from the Kansas Weather Data Library, vegetation and soil data from the USDA, and current land-use management practices. Results show that mean annual precipitation (from 1985–2005) is partitioned into 13% runoff regionally and 14% locally over the Konza LTER, lateral flow through soil is 1% regionally and 2% locally, groundwater recharge is 11% regionally and 9% locally, and evapotranspiration accounts for the remaining 75%. The spatial distribution of recharge was used in a regional Modflow groundwater model that was calibrated to existing groundwater observations and field measurements gathered for this study, giving a hydraulic conductivity in the Flint Hills region of 1–2 m day 1 with a local zone (identified here) of 0.05–0.1 m day 1. The resistance was set to fixed representative values during model calibration of hydraulic conductivity, and simple log-log relations correlate the enhanced recharge beneath ephemeral upland streams and baseflow in perennial lowland streams to the unknown resistance of the streambeds. Enhanced recharge due to stream transmission loss (the difference between terrestrial runoff and streamflow) represents a small fraction of streamflow in the ephemeral upland and the resistance of this streambed is 100 000 day. Long-term baseflow in the local Kings Creek watershed (2% of the groundwater recharge over the watershed) is met when the resistance of the lowland streambed is 1000 day. The coupled framework developed here to study surficial ecohydrological processes using EPIC and groundwater hydrogeological processes using Modflow provides a baseline hydrologic assessment and a computational platform for future investigations to examine the impacts of climate change, vegetative cover, soils, and management practices on hydrologic forcings.