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Both sporadic observations and modelling studies suggest that subthermocline eddies (SEs) exist east of the Philippines, where interhemispheric waters meet. However, effects of SEs on water mass mixing have never been observed. Here, using data from mooring and buoy deployed in the frontal region of the interhemispheric water masses, we show for the first time that the SEs act as an “underwater mixer” of intermediate waters from north and south Pacific oceans. The SEs have typical swirl speeds of 0.1~0.4 m s −1  between 200 and 800 m depth with a dominant period of ~90 days. Variation in intermediate water salinity also had a period of ~90 days, lagging eddy speed by ~8 days. Horizontal eddy diffusivity representative of eddy mixing rate was quantified using a mixing-length framework. Horizontal eddy diffusivity had both surface and subthermocline maxima. The vertically varying eddy diffusivity can be used to improve parameterization of eddy stirring in the tropical Pacific by coarse-resolution ocean climate models. The effect of the SEs on mixing of intermediate water masses seems not resolved by available eddy-resolving ocean models typically used for this region.

Isopycnal mixing of interhemispheric intermediate waters by subthermocline eddies east of the Philippines