Suspended Particulate Matter (SPM), surface (bed sediments) and short length cores of sediments collected from the largest tributary of the river Ganges, namely the river Yamuna, were analysed for total mercury as well as its fractionation in various size and chemical sites in the sediments following standard procedures. Also, attempts were made to determine the vertical distribution in sediments in relation to the recent timescale of a few decades. Our observations indicate that the SPM in general showed higher levels of total mercury compared to the surface sediments while at places the enhancement could be by a factor of 10, say around 25 microg g(-1) in the downstream region that integrates the industrial midstream and agricultural downstream terrain near its confluence with the Ganges. Surface sediments in the upstream direction near the Himalayan foothills and SPM in the lower reaches showed significant high Index of Geoaccumulation (Igeo) as defined by Müller. Size fractionation studies indicate that the finer fraction preferentially showed higher levels of mercury while in the lower reaches of the river, the total mercury is equitably distributed among all size fractions. The proportion of the residual fraction of mercury in relation to mobile fractions, in general decreases downstream towards its confluence with the Ganges river. In sediment cores, the vertical distribution show systematic peaks of mercury indicating that addition of this toxic metal to the aquatic system is in direct proportion to the increase in various types of human activities such as thermal power plants, land use changes (urbanisation) in the midstream region and intensive fertiliser application in lower reaches of this vast river basin.