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The standard gravest empirical mode (GEM) technique for utilizing hydrography in concert with integral ocean measurements performs poorly in the southwestern Japan/East Sea (JES) because of a spatially variable seasonal signal and a shallow thermocline. This paper presents a new method that combines the U.S. Navy's Modular Ocean Data Assimilation System (MODAS) static climatology (which implicitly contains the mean seasonal signal) with historical hydrography to construct a “residual GEM” from which profiles of such parameters as temperature (T) and specific volume anomaly (δ) can be estimated from measurements of an integral quantity such as geopotential height or acoustic echo time (τ). This is called the residual GEM technique. In a further refinement, sea surface temperature (SST) measurements are included in the profile determinations. In the southwestern JES, profiles determined by the standard GEM technique capture 70% of the T variance and 64% of the δ variance, while the residual GEM technique using SST captures 89% of the T variance and 84% of the δ variance. The residual GEM technique was applied to optimally interpolated τ measurements from a two-dimensional array of pressure-gauge-equipped inverted echo sounders moored from June 1999 to July 2001 in the southwestern JES, resulting in daily 3D estimated fields of T and δ throughout the region. These estimates are compared with those from direct measurements and good agreement is found between them.