This paper introduces a new method for finding the top of thermocline (TTD) and halocline (THD) depths that may become a powerful tool for applications in shallow marine basins around the world. The method calculates the moving average of the ocean vertical profile’s short-scale spatial variability (standard deviation) and then processes it to determine the potential depth at which temperature or salinity rapidly changes. The method has been calibrated using an extensive set of data from the ecohydrodynamic model EcoFish. As a result of the calibration, the values of the input parameters that allowed the correct determination of TTD and THD were established. It was confirmed by the validation carried out on the in situ profiles collected by the research vessel S/Y Oceania during statutory cruises in the southern Baltic Sea. The “MovSTD” algorithm was then used to analyze the seasonal variability of the vertical structure of the waters in Gdańsk Deep for temperature and salinity. The thermocline deepening speed was also estimated in the region analyzed.
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