The Southwest Monsoon Current (SMC) flows eastward from the Arabian Sea into the Bay of Bengal (BoB) during summer, advecting a core of high salinity water. This high salinity core has been linked with Arabian Sea High Salinity Water that is presumed to enter the BoB directly from the Arabian Sea via the SMC. Here we show that the high salinity core originates primarily from the western equatorial Indian Ocean, reaching the BoB via the Somali Current, the Equatorial Undercurrent and the SMC. Years with anomalously saline high salinity cores are linked with the East Africa Coastal Current and the Somali Current winter convergence, and an anomalously strong Equatorial Undercurrent. Seasonal reversals that occur at the Somali Current and SMC junctions act as 'railroad switches' diverting water masses to different basins in the northern Indian Ocean. Interannual fluctuations of the Equatorial Undercurrent are linked to wind stress and El Nino.