AbstractThe discharge of freshwater from major rivers into the northern Bay of Bengal (BoB) increases dramatically during the summer monsoon season, reaching a peak in August–September, and there is a corresponding increase in the vertical salinity gradient in the upper ocean. Here we study the impact of seasonally evolving near‐surface salinity stratification on the response of ocean mixed layer temperature (MLT) to Summer Monsoon Intraseasonal Oscillations (MISO), using accurate surface fluxes and high vertical resolution (∼2 m) hydrographic measurements from a mooring in the northern BoB (17.8°N, 89.5°E) during June–September 2019. Prominent MLT warming and cooling with a range of 1.5°C is observed between suppressed (clear skies, calm winds) and active (cloudy, windy) phases of MISO convection. However, the intraseasonal MLT response to the active phase of a late‐season MISO event is minimal compared to MISO events in early summer. We infer this is primarily due to the much smaller contribution from oceanic vertical processes (∼6 Wm−2) in late summer 2019, compared to their role in early summer (−15 to −55 Wm−2). During the active phase of the MISO event of late summer 2019, the combined effect of reduced entrainment and weak vertical temperature gradients associated with a barrier layer inhibits near‐surface cooling. Conversely, the near‐surface salinity stratification and the barrier layer are weak during MISO events in the early summer of 2019—these hydrographic conditions lead to enhanced MLT cooling in response to MISO, apparently through a freer turbulent exchange of cool thermocline water with the surface layer.