To gain a better understanding the sedimentological behaviour in the estuarine, coastal environment and their distribution patterns in trace elements in the estuary and to examine variations in associated sediment fluxes, 20 surface samples were collected throughout the Manakudy estuary, a minor Pazhayar river in south-western India. These samples, collected in typical dry season during Premonsoon 2012, were analyzed for Sedimentological, Textural and Trace Elements (HOAc). Our results show that estuary is dominated by sand fraction of the sediments (72.68%), the conservative behavior of trace metals with salinity has been strongly has been affected by the introduction of these metals by external sources and they are due to the higher organic activity in soils as well as faster rates of chemical weathering reaction in the source region. Even though the trace metals in the contaminated sediments have been removed and incorporated in sediments due to flocculation, the concentration of these metals did not decrease. The present study provides a history of accumulation of trace metals and their present level, and the data can be used as a baseline to monitor the estuaries environments.