Variation in sedimentology as well as freshwater and marine palynomorphs has been studied in ecological perspective in two 2.5- and 5-m deep sediment cores deposited since 3440 and 3630 cal BP, respectively in the central part of Pichavaram mangrove wetland, Cauvery River delta. The palynological and sedimentological results of the sediments reveal a monsoonal circulation and a climatic shift from warm and humid with strengthened monsoon (3630–3190 cal BP) to dry and arid (~2750–760 cal BP). Since the last millennium (~760 cal BP), Pichavaram estuary has been influenced by a similar cyclicity but with a less wet and humid climate due to weakened monsoon conditions. These ecological changes in turn affect the relative sea level rise and fall which is reflected by the variability/extinction of freshwater and marine palynomorphs. The estuary remained an active water channel between ~3630 and 2750 cal BP, responding to the strengthened monsoon, during which the freshwater algal remains with thecamoebians and marine dinoflagellate cysts and foraminiferal linings both dominated with a ratio of 1.5 for marine/freshwater forms. After this period, since ~2750 cal BP there has been a dominance of marine forms with a ratio of 4.5 for marine/freshwater forms, indicating fluvio-marine sediment deposition and suggesting the recent landward intrusion of seawater during weakened monsoon conditions. Freshwater thecamoebians are vulnerable to the salinity >3 in the aqueous soil solution of estuarine sediment, and therefore serve as an excellent proxy for monitoring salinity gradient along with short-term high resolution palaeoecological fluctuations induced by climate and relative sea-level changes in an estuarine ecosystem.