We use satellite-derived currents and a Lagrangian approach to investigate the redistribution of the precipitation minus evaporation (P-E) and river freshwater inputs into Bay of Bengal (BoB) by the oceanic circulation. We find a key role of Ekman transport in shaping the BoB freshwater distribution. Until September, the summer monsoon winds induce eastward Ekman transport, which maintains freshwater near its major rivers and rain sources in the northeastern BoB. The winter monsoon Ekman transport strongly contributes to the surface flow in many areas of the interior BoB. This ~ 0.15 m s−1 westward transport overcomes the weaker offshore transport by mesoscale motions and pushes a ~ 40/45% mixture of P-E and Ganges–Brahmaputra freshwater into the East Indian Coastal Current (EICC). In agreement with previous studies, we find that the EICC then transports Ganges–Brahmaputra freshwater southward, allowing the formation of a narrow freshwater tongue or “river in the sea” along the coast east of India in November. Ekman transport thus operates jointly with the EICC to allow the “river in the sea” formation. The EICC is nonetheless a “leaky pipe” as only ~ 22% of the Ganges–Brahmaputra, and ~ 9% of the P-E monsoonal freshwater inputs exit the BoB near Sri Lanka. The winter monsoon anticyclonic circulation in fact brings more rain freshwater from the equatorial Indian Ocean into the southeastern BoB than it exports freshwater through the EICC. As a result, the BoB circulation contributes to a net freshwater gain that amounts to 11% of the local rain and freshwater inputs.