To understand the chlorophyll-a distribution in the neritic waters of the northern Indian Ocean, which comprises the Arabian Sea on the west and the Bay of Bengal on the east, seawater samples were collected during early north-east monsoon season (November, 2008). The column integrated chlorophyll-a over the Arabian Sea and the North Bay of Bengal exhibit high concentrations. However, the southernmost station (0806) shows enhanced chlorophyll-a concentration compared to other stations in the south Bay (0807, 0808 and 0809). This is attributed to eddy pumping of nutrients from subsurface to surface waters of the Bay during the study period due to cyclonic conditions. This observation is further supported by the lack of nutrients in the surface waters at the other stations from the south Bay compared to the station 0806, which has high nutrient concentrations. The observed salinity in the Bay of Bengal shows a strong north-south gradient with higher salinity in the southern part of the Bay. The supply of nutrients through fluvial input (that is, dominantly from the northern region) is insignificant. The enhanced chlorophyll-a concentration over the farthest station (0806) can be either due to Eddy mediated biological production or lateral advective transport of nutrients.