A new algorithm is presented for estimating salinity profiles in the upper ocean from measurements of temperature profiles and surface salinity. In application to the eastern tropical Pacific the method replicates a large fraction of the variability of salinity in the upper few tens of meters and provides modest to substantial improvement at nearly all levels. Estimated salinity profiles are able to characterize barrier layers, regions formed by a halocline within the thermal mixed layer. The rms error of geopotential height calculations based on estimated salinity profiles is reduced more than 50% by this method relative to methods not using surface salinity. Even without the surface salinity measurement some reduction of error in geopotential heights can be obtained relative to previous methods. ¿ 1999 American Geophysical Union