Palaeoclimate and palaeoecological study was carried out using palynological and thecamoebian evidences buried in ~ 4 m vertically exposed sediment section (12 km inland from the present shoreline) of Late Holocene age along the banks of Gautami-Godavari River and from three shallow cores from its Nilarevu tributary, Andhra Pradesh. Inferred climatic periods include (1) a basal cold/arid period (~3000-2000 yrs BP) with dominance of Botryococcus and other fresh water algal remains coupled with abundance of 25 species of thecamoebians indicating shallow and lentic ecosystem during most of the period and (2) a relatively warm/wet conditions (since ~2000 yrs BP) reveal lotic fresh water ecosystem characterized by the evidences of tree palynotaxa and low percentage of thecamoebians. The three shallow cores (0.5 -1 m) near the mouth (~8 km stretch) of the Nilarevu tributary reveal fluvio-marine deposition in the top 50-80 cm sediment unlike the deeper fresh water depositional environment suggesting sea water ingression in the recent decades. The study illustrates that the Gautami-Godavari River delta gradually prograded since ~3000 yrs BP until 100-150 yrs unlike the intermittent relative sea level rise and fall recorded during the same period in the contemporary south-east deltaic areas.