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A method for providing a more accurate synthetic profiles of temperature, salinity and sound speed of the ocean over an area of interest is provided by using a value of the mixed layer depth in addition to values of surface temperature and surface height in an ocean modeling system such as the Modular Ocean Data Assimilation System (MODAS) system developed for the U.S. Navy. The method of the present invention compares the predicted or observed mixed layer depth for the area of interest, for example, as obtained from remote sensing or upper ocean modeling, to a mixed layer depth estimated from an initial synthetic profile, and determines which is deeper, termed the reference mixed layer depth. The method then derives a modified temperature and salinity synthetic profile by setting the temperature and salinity equal to the surface values at depths less than or equal to the reference mixed layer depth and using an algorithm to estimate temperature and salinity at depths below the reference mixed layer depth.