This study examines the future climate change in the South Asia region during 2070–2099 with respect to the historical period (1975–2004) under RCP8.5 scenario using a high-resolution regional earth system model. We found substantial changes in the key climatic parameters over the South Asia region including ocean biological productivity, however, the magnitude of response varies spatially. A substantial increase (> 2.5 °C) in the projected annual-mean sea surface temperature (SST) was found over the Indian Ocean with the highest increase (~ 3.4 °C) locally in the northern part of the Arabian Sea and in the Persian Gulf, SST changes being significant throughout the study area with 95% confidence level. The changes in the sea surface salinity showed strong spatial variability with the highest freshening over northern Bay of Bengal and highest salinity in the Persian Gulf followed by northern Arabian Sea. The amount of annual-mean precipitation will substantially increase over the eastern coast of the Bay of Bengal (up to 1.5–2.0 mm/day) and along the equator in the band 10° S–10° N (0.5–1.5 mm/day), while it will decrease over the western part of the Bay of Bengal and in the northern states of India (− 0.5 to 1.0 mm/day). The most pronounced increase of precipitation rate in the future climate will occur over India (3–5 mm/day) and the eastern coasts of the Bay of Bengal (> 5 mm/day) during the monsoon period, and over the equatorial band (2–3 mm/day) during the post-monsoon period, with all precipitation changes indicated above being significant at 95% confidence level.