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Interaction between groundwater and surface water in watersheds has significant impacts on water management and water rights, nutrient loading from aquifers to streams, and in-stream flow requirements for aquatic species. Of particular importance are the spatial patterns of these interactions. This study explores the spatio-temporal patterns of groundwater discharge to a river system in a semi-arid region, with methods applied to the Sprague River Watershed (4100km(2)) within the Upper Klamath Basin in Oregon, USA. Patterns of groundwater-surface water interaction are explored throughout the watershed during the 1970-2003 time period using a coupled SWAT-MODFLOW model tested against streamflow, groundwater level and field-estimated reach-specific groundwater discharge rates. Daily time steps and coupling are used, with groundwater discharge rates calculated for each model computational point along the stream. Model results also are averaged by month and by year to determine seasonal and decadal trends in groundwater discharge rates. Results show high spatial variability in groundwater discharge, with several locations showing no groundwater/surface water interaction. Average annual groundwater discharge is 20.5m(3)/s, with maximum and minimum rates occurring in September-October and March-April, respectively. Annual average rates increase by approximately 0.02m(3)/s per year over the 34-year period, negligible compared with the average annual rate, although 70% of the stream network experiences an increase in groundwater discharge rate between 1970 and 2003. Results can assist with water management, identifying potential locations of heavy nutrient mass loading from the aquifer to streams and ecological assessment and planning focused on locations of high groundwater discharge. Copyright (c) 2016 John Wiley & Sons, Ltd.