Mean sea level rise (MSLR) and weather extremes can drive extreme sea level (ESL) variations locally. In the Indian Ocean, ESL estimates under global warming are either absent or limited by MSLR alone or biased storm surge model simulations. Using tide gauge, machine learning, and numerical models, we identify a rapid emergence of ESL in the Indian Ocean, particularly in the equatorial region compared to off-equatorial areas. Equatorial islands will experience the one-in-a-hundred-year ESL (ESL100) of the present-day annually by 2030-40 under a high-emission scenario, with delay until 2050 for the Arabian Sea coastline and the south subtropical regions. MSLR will mainly contribute to future ESL changes, with tide and surges contributing less than 10%. A median rise of 60–80 cm in ESL is anticipated by 2100, demanding coastal planning and climate adaptation strategies for a resilient coastal population.