Abstract Rainfall variability in the Tigris–Euphrates headwaters is a result of interaction between topography and meteorological features at a range of spatial scales. Here, the Weather Research and Forecasting (WRF) Model, driven by the NCEP–DOE AMIP-II reanalysis (R-2), has been implemented to better understand these interactions. Simulations were performed over a domain covering most of the Middle East. The extended simulation period (1983–2013) enables us to study seasonality, interannual variability, spatial variability, and extreme events of rainfall. Results showed that the annual cycle of precipitation produced by WRF agrees much more closely with observations than does R-2. This was particularly evident during the transition months of April and October, which were further examined to study the underlying physical mechanisms. In both months, WRF improves representation of interannual variability relative to R-2, with a substantially larger benefit in April. This improvement results primarily from WRF’s ability to resolve two low-level, terrain-induced flows in the region that are either absent or weak in R-2: one parallel to the western edge of the Zagros Mountains, and one along the east Turkish highlands. The first shows a complete reversal in its direction during wet and dry days: when flowing southeasterly it transports moisture from the Persian Gulf to the region, and when flowing northwesterly it blocks moisture and transports it away from the region. The second is more directly related to synoptic-scale systems and carries moist, warm air from the Mediterranean and Red Seas toward the region. The combined contribution of these flows explains about 50% of interannual variability in both WRF and observations for April and October precipitation.