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This study delineates the role of small and medium river inputs, Low Saline Plume Advection (LSPA) and eddies in hydrography alteration and Chlorophyll a (Chl. a) in the Western Bay of Bengal. Samples were collected across five transects viz: Hooghly (HO), Mahanadi (MN), Rushikulya (RK), Visakhapatnam (VSKP) and Godavari (GD) during Fall Intermonsoon. Each transect consists of 7 or 8 locations from inshore to offshore. LSPA propagates southward concordance with the East India Coastal Current (EICC) and its southward flow strengthened by a cold-core eddy. LSPA results in the intermittent low salinity in the cross-shore section of HO, MN and RK. Upper layer Chl. a is 2–3 folds higher in inshore and in LSP-influenced locations than in its adjacent stations. The present study identified Double Chlorophyll a Maxima (DoCM) in LSPA-influenced slope regions of MN and RK. DoCM is less known in the BoB. DoCM has both the Surface Chl. a Maxima (SCM) and Subsurface Chl. a Maxima (SSCM). SSCM layer is relatively shallow and intense in slope and offshore regions of MN and RK due to their closeness with cold-core eddy. The present study highlights that freshwater discharge from small and medium rivers impacts hydrobiology around 10–50 km from the shore depends on the magnitude of river influx. LSPA is away from the local inputs and impacts hydrobiology (>500 km) along the path. EICC and eddies together regulated the direction of LSPA. Existing eddies nature alters vertical hydrobiology in slope and offshore regions.