Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) 2A25 reflectivity profiles data during the period 1998–2013 are used to study the differences in the vertical structure of precipitation and its variation with sea surface temperature (SST) over the Arabian Sea (AS) and the Bay of Bengal (BOB). Even though the AS and the BOB are parts of the Indian Ocean, they exhibit distinct features in vertical structure of precipitation and its variation with SST. The variation of reflectivity and precipitation echo top occurrence with SST is remarkable over the AS but trivial over the BOB. The median reflectivity increases with SST at all heights below 10 km altitude, but the increase is prominent below the freezing level height over the AS. On the other hand, irrespective of altitude, reflectivity profiles are same at all SSTs over the BOB. To understand these differences, variation of aerosols, cloud and water vapor with SST is studied over these seas. At SSTs less than 27 °C, the observed high aerosol optical depth (AOD) and low total column water vapor (TCWV) over the AS results in small Cloud effective radius (CER) values and low reflectivity. As SST increases AOD decreases and TCWV increases, which result in large CER and high reflectivity. Over the BOB the change in AOD, TCWV and CER with SST is marginal. Thus, the observed variations in reflectivity profiles seem to be present from the cloud formation stage itself over both the seas.