The interannual variability of rainfall caused by the El Niño Southern Oscillation (ENSO) results in significant changes in hydrologic conditions that affect entire countries’ water supply. Forecasting ENSO and its impacts are mainly based on Central Pacific Sea surface temperature (SST) anomalies which satisfactorily correlates with timing and, to a lesser extent, the intensity of drought conditions in the Philippines and the rest of the Western Pacific during the El Niño phase. Changes in sea surface height (SSH) are also brought upon by ENSO through density changes with temperature and oceanographic processes. Here, we report that the associative nature of SSH and drought as measured by surface runoff, has a stronger correlation (r > 0.693, p < 0.05) in terms of the expected timing, with 1 to 3 months lag time, and intensity compared to using traditional ENSO SST indices from the Central Pacific. Furthermore, since SSH is co-located with its corresponding forecasted decrease in runoff, a localized prediction can be made which further increases the accuracy of this predictive tool. In the wake of a changing climate, this work demonstrates the possibility of statistically forecasting the timing of precipitation, and thus the volume of surface water availability, using local SSH as an indicator. A tool which is necessary for time-sensitive management decision making in drought-prone tropical regions.