Many previous studies have documented the changes in rainfall patterns along the Western coast of India. The Western Ghats of India comprising of coastal regions of Maharashtra, Karnataka, and Kerala regions are facing the worst floods and droughts in recent years. Changes in low-level horizontal wind circulation due to the change in sea surface temperature over the northern Arabian Sea have been reported by many studies. This work highlights the role of surface–subsurface variations in temperature over the Arabian Sea in governing rainfall variability over the Western Ghats. The subsurface flow of water masses from the Southern Indian Ocean into the Arabian Sea or vice versa along the Somalia–Oman coast can increase or decrease the depth of the thermocline. Deepening or shoaling of thermocline depth in the central Arabian Sea can further lead to changes in the surface temperatures. The rainfall variability over the Western Ghats is predominantly governed by the sea surface temperature (SST) variations over the Arabian Sea. The shoaling of thermocline due to an increase in Ekman upwelling and decrease in the subsurface water flow has decreased SST in the Arabian Sea in the recent decade. This decrease in SST can lead to a decrease in the rainfall over the Western Ghats. This study also reports an interdecadal oscillation in the surface-subsurface coupling over the Arabian Sea.