Transboundary basins in arid and semi-arid regions are increasingly stressed by groundwater depletion, drought, and competing upstream water-management policies. Quantifying surface-groundwater interactions in such systems remains challenging due to sparse hydroclimatic observations. This study develops and applies a fully coupled SWAT-MODFLOW model to the Tigris-Euphrates River Basin (TERB; similar to 900,000 km(2)), the largest transboundary basin in the Middle East, to evaluate spatiotemporal stream-aquifer interactions and basin-scale water balance. The model integrates SWAT 2012 with MODFLOW-NWT at daily and monthly time steps and was calibrated and validated against monthly streamflow records from 23 gauges and groundwater levels from four wells over 1981-2002, with a 1976-1980 warm-up period. A multi-stage calibration strategy was adopted, including standalone SWAT calibration using SUFI-2, standalone MODFLOW calibration using PEST, and subsequent coupled refinement. Model performance was satisfactory, with Nash-Sutcliffe efficiencies exceeding 0.5 for streamflow and strong agreement between simulated and observed groundwater levels (R-2 = 0.92). Basin-integrated total water storage anomalies showed reasonable agreement with GRACE-derived estimates for 2002-2013 (R-2 approximate to 0.72). The basin-averaged net stream-aquifer exchange was estimated at -7.08 x 10(6) m(3) yr(-1), indicating net river leakage to aquifers, with a marked intensification after 1987 consistent with major upstream reservoir developments. Recharge patterns were highest over permeable foothill formations and lowest over consolidated northern highlands. The integrated use of streamflow, groundwater, and GRACE observations within a fully coupled framework provides a transferable approach for water-resources assessment in data-scarce transboundary basins.