The effect of river runoff over the north Indian Ocean (NIO) especially over the Bay of Bengal (BoB) has beenstudied using global Nucleus for European Modelling of the Ocean (NEMO). Two sensitivity experiments, with and without river runoff are conducted and the influence of river runoff on the Indian Ocean hydrography, stratification and circulation features are studied. It is found that due to river runoff surface salinity over the north BoB decreases by more than 5 and the East India Coastal Current strengthens by 2 cm/s during post monsoon season. The fresh river water reaches up to 15°N in the BoB and is the main cause for low salinity there. Sea surface temperature in the northwest BoB increases by more than 0.2°C due to the river runoff in summer monsoon while surface cooling upto 0.2°C is seen in north-west part of BoB in winter season. The seasonal mixed layer depth in the region is found to be dependent on river runoff. The effect of vertical shear and Brunt Vaisala frequency on stratification is also examined. The ocean water becomes highly stratified up to 3035 m due to the river runoff. It is found that the energy required for mixing is high in the north and coastal BoB.