An empirical parameterization for Se is proposed and tested in an intermediate ocean model (IOM) of the Tropical Pacific Ocean. An inverse modeling approach is first adopted to estimate Se from a sea surface salinity (SSS) anomaly (SSSA) model using observed in-situ SSS measurements, simulated upper ocean currents, and freshwater flux (evaporation minus precipitation, E-P) data. A relationship between Se and sea level (SL) anomalies is then obtained by utilizing an empirical orthogonal function (EOF) technique. This empirical scheme is able to estimate Se anomalies reasonably well in the equatorial Pacific Ocean and can be used to parameterize Se fields in terms of SL anomalies for use in SSSA calculations. An optimized Se parameterization naturally leads to a balanced depiction of the subsurface effect on SSS variability in association with entrainment and vertical mixing. As a result, SSSA simulations can be potentially improved in the Tropical Pacific.