This research assesses the impacts of climate change and relative sea level (RSL) fluctuations on coastal vegetation during the past 2000 years along the Mahanadi River delta, northeast coast of India. Sediment samples of a 2.6 m trench from Barhatubi area located in the lower flood plain of Mahanadi River delta were studied for sedimentological and pollen analysis. Mangrove succession can be divided into three zones: (1) Freshwater marsh (∼1980–1420 cal yr BP); (2) Tidal flat (∼1420–770 cal yr BP) and (3) Landward mangrove margin (∼770 cal yr BP-Present). A transgressive shift from floodplain freshwater marsh to a tidal flat is recorded between ∼1980–1420 cal yr BP which is evidenced by upland tree taxa, Poaceae, pteridophyte and fungal spores along with low percentage of mangroves such as Avicennia, Sonneratia and Rhizophora representing the landward edge of the tidal region. Dominance of Sonneratia and a decline in terrestrial taxa reflects a rise in the relative sea level around ∼1420 cal yr BP with less freshwater input from land suggesting a weakened monsoon condition. After ∼770 cal yr BP, an overall regressive phase with small cycles of relative sea level rise/fall has been observed due to the dominance of salt tolerant Avicennia along with Rhizophora, Excoecaria agallocha and Aegialitis rotundifolia alternating with Sonneratia and other marine palynomorphs.