In situ and satellite sea level data sets over 1980–1998 are used to estimate interannual variations of the geostrophic zonal transport from the western Pacific Ocean into the Celebes Sea. Then the transport component due to the Pacific wind-driven and fully reflected equatorial waves is removed. Finally, the residual variations, named Indonesian throughflow correction (ITFC), are used to correct for the model closed western boundary. ITFC inflows/outflows are leading the warm/cold events by a few months. They are then prescribed at the model western boundary over 1980–1998 to compare with closed boundary simulations. An ITFC inflow anomaly makes the eastern Pacific slightly warmer and trade winds in the central Pacific slightly weaker. Indeed, these quantities are simulated by both experiments in very good agreement with observations. More importantly, prescribing the ITFC greatly improves two characteristics of the model that play a key role in the coupled simulations. The first is the RMS variability of sea level versus longitude; the ITFC shifts to the west the position of the minimum. The second is the basin average sea level; the ITFC largely amplifies its fluctuations, stimulating the charge and discharge of the system. Consequently, the ITFC can have a very large impact on El Niño-Southern Oscillation forecasts. For example, the 1982/1983 and 1997/1998 1-year lead forecasts which fail to predict the warm events with closed boundaries are successful with the ITFC. The impact of the ITFC on coupled simulations is not linearly dependent on the ITFC value itself: In addition to the fluctuating conditions at the western boundary, results depend on how close to instability the system is at each time step.