The rare-earth elements (REE), La to Lu, are widely used as tracers of geochemical processes in a wide variety of sedimentary environments. REE are useful for determining petrogenetic histories of rocks (Shields and Stille, 2001). Several investigators reported dissolved and particulate REE in fluvial systems and identified the influence of weathering on fractionation of REE and yttrium (Nesbit, 1979; Nesbit et al., 1990; Nozaki et al., 1997; Andersson et al., 2006; Ma et al., 2007) and control of source rock composition on REE of sediments (Singh and Rajamani, 2001; Yang et al., 2002). The dissolved and particulate REE are affected by both flocculation and precipitation processes at the mixing zone of fluvial and seawater. Geochemical processes identified at this stage are large scale removal of dissolved fluvial REE (in particular light REE) (Sholkowitz and Szymezak, 2000; Nozaki et al., 2000), salt-induced coagulation of river colloids (Elderfield et al., 1990) and REE adsorption on Fe-organic colloids (Sholkovitz and Elderfield, 1988; Sholkovitz, 1993) and particulate organic carbon (Byrne and Kim, 1990; Sholkovitz, 1992; Schijf et al., 1995; Arraes-Mescoff et al., 2001; Haley et al., 2004). Fractionation of REE, especially light to heavy REE and Ce relative to other REE develops in a river-estuarine system. Although Y and Ho have similar ionic radii, the seawater ratios of Y/Ho are approximately 2 times higher than the crustal values (Nozaki et al., 1997), suggesting fractionation of Y and Ho must take place during weathering and riverine transport or in marine conditions. Bau et al. (1995) suggested fractionation of Y to Ho takes place largely in rivers and estuaries, whereas Nozaki et al. (1997 and 2000) suggested most prominent fractionation in estuaries and seawater. Although both Sm and Nd are mobile during weathering, REE-bearing minerals and differential weathering of constituent minerals, for instance removal of less susceptible minerals like feldspar, would grossly change the Sm/Nd ratio. Therefore the Sm/Nd ratio of the weathered soil depends on primary residual phases and secondary phases produced during transformation of rock to a soil layer (Viers and Wasserburg, 2004; Bau and Zhao, 2008; Feng, 2010). Several investigators identified the factors (source rock composition, grain size and mineralogy) that control REE distribution in surficial sediments (Cullers et al., 1987; Klaver and van Weering, 1993; Yang et al., 2002; Borrego et al., 2005; Censi et al., 2007; Prego et al., 2009; Jung et al., 2012). There are a few studies on cycling of REE during early diagenetic decay of organic matter in estuarine sediments (López-González et al., 2012; Morgan et al., 2012). Investigations on marine sediments have revealed the REE patterns in sedimentary systems are influenced by both depositional environment (Murray et al., 1990, 1992) and diagenetic processes (Milodowski and Zalasiewicz, 1991; Murray et al., 1992). Nozaki et al. (2000) suggested Nd and other REE are released back to seawater from sediments in high salinity regions of estuaries. Therefore, the REE that reach the oceans are the products of source rock composition, fractionation during weathering and sum of geochemical (depositional and diagenetic) processes in estuaries. Investigations on bottom sediments of the estuaries help us to understand the processes involved in controlling the distribution and fractionation of REE. The purpose of this paper is to report the down core distribution of REE and Y in four sediment cores collected along transect of the Mandovi estuary, western India (Fig. 1) and to determine the factors controlling their distribution and fractionation.