Many dammed reservoirs in dry climate conditions witness high sediment inflow rates due to higher soil erodibility, yet there are limited actual sediment influx measurements. Therefore, this study first applies the Soil and Water Assessment Tool (SWAT) hydrologic model to simulate reservoir sedimentation inflow to the Haditha Reservoir. Next, utilizing sediment inflows estimated by the SWAT model, the Trap Efficiency Function (TEF) is employed to estimate its remaining storage capacity and its useful life at multiple reservoir water levels. Calibration (1986–1997) and validation (1998–2007) of the SWAT model were conducted at three streamflow gaging stations and one sediment station located upstream of the reservoir. Results show that the SWAT model performed better during calibration than during the validation period for all streamflow and sediment gaging stations. In addition, modeled streamflow and sediment predictions were relatively more accurate on a monthly scale than on a daily scale. Simulated daily sediment inflow to the reservoir demonstrates slightly lower accuracy than daily streamflow, where the Coefficient of Determination (R²) and Nash-Sutcliffe Efficiency values are 0.34 and 0.32 in the case of sediment load, compared to 0.39 and 0.33 for streamflow, respectively. Reservoir storage capacity for the period (1986–2005) shows a continuous decrease with time at all reservoir water levels, which indicates an increase in sediment accumulation. According to measurements taken between 1986 and 2005, sediment accumulation has reduced the reservoir’s capacity by approximately 15% at a water level of 112 m (the lowest water level in the reservoir). During the same period, the storage capacity loss at 147 m (the design working water level in the reservoir) was calculated to be 35%. Over 19 years of operation (1986–2005) at the 147-m water level, the total sediment buildup in the reservoir is estimated at 3.2 million tons. Notably, about one-third of this sediment was deposited in the five-year span from 2000 to 2005.

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; ~900,000 km²), 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 (R² = 0.92). Basin-integrated total water storage anomalies showed reasonable agreement with GRACE-derived estimates for 2002–2013 (R² ≈ 0.72). The basin-averaged net stream–aquifer exchange was estimated at −7.08 × 10⁶ m³ 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.