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Abstract The Northern Indian Ocean (NIO) experiences strong upper ocean warming during the spring intermonsoon season, with nearly 90% of the days showing net heat gain. However, observations reveal spatially heterogeneous Sea Surface Temperature (SST) trends [O(1°C) differences] in these regions over intra‐seasonal timescales (15–45 days) and mesoscale and smaller length scales (<100 km), coinciding with significant lateral variability in winds [O(2 m s −1 )] and salinity stratification [O(2 g kg −1 ) in surface salinity and O(20 m in mixed layer depth)]. This study investigates the role of salinity‐driven mixed layers in driving these gradients in foundational SST warming using one‐dimensional modeling. Simulation results using realistic surface forcing show that lateral differences in stratification result in spatial differences in warming of foundational SST by about 0.2–0.5°C over 14–21 days, specifically for shallow mixed layers. However, the influence of stratification on foundational SST warming is nuanced and varies across the NIO, leading to either enhanced or reduced warming. Idealized simulations show that this contrast depends on net heat flux and water optical properties, with stratified cases warming more under high fluxes and turbid conditions. To generalize, we derive an analytical expression for the crossover heat flux , the threshold at which stratified and unstratified cases warm equally. depends on shortwave radiation, mixed layer depth and optical properties. For representative clear‐sky conditions, ranges from 103 to 136 W m −2 . These findings underscore the role of salinity‐driven stratification and bio‐optical feedback in shaping SST gradients, with likely implications for sub‐seasonal to seasonal monsoon forecasting.