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Thermohaline structure of Kochi backwaters under fair and rough weather conditions has been examined along with thermal structure of two open-ocean islands in the adjoining southeastern Arabian Sea (Kavaratti and Andrott in the Lakshadweep Archipelago). Longitudinal thermohaline structure of Kochi backwaters was found to be inhomogeneous, where the relatively warm and low-saline head estuary gets easily disturbed by sudden changes in meteorology, manifested by a sharp drop in temperature and salinity. The southernmost location was the most sensitive, and the easternmost location the least sensitive to meteorological changes. Thermohaline stratification was greater at the mouth region during monsoon, where a cap of (∼4 m) low-saline water (⩽2 psu) floats over a thermal gradient of ∼3.5°C (9 m depth). Spring-neap thermohaline behaviour exhibited weak inverse correlation (R² ⩽ 0.58), with a relative cooling due to the incursion of seawater during spring tide. However, a stronger correlation was observed between salinity and tide (R² = 0.64). The thermal variations were mainly attributed to day/night heating/cooling processes, tides and winds. The cooling of island waters due to wind was delayed by half a day, whereas that of the Kochi backwaters was delayed by more than 1.5 days. Temperature variability at the Kochi backwaters was also influenced by its shallow depth, surrounding land mass and vegetation on its periphery. The mouth of the estuary was additionally cooled by upwelled waters from the Arabian Sea. [ABSTRACT FROM AUTHOR]