The land-sea interface is considered as a threatening environment due to anthropogenic development activities. Unplanned developments can cause effects on important ecosystems, water and human health as well. In this study, the influence of rapid regional development on the accumulation of trace elements to the sediments of an important ecosystem, Batticaloa lagoon, Sri Lanka was examined. Surface sediment pollution status and ecological risk was compared with that of the recent sedimentary history of about 1 m depth. Sediment core samples were collected and analyzed for grain size, organic matter and carbonate contents and trace elements (As, Pb, Zn, Cu, Ni and Cr) by the X-Ray Fluorescence (XRF) technique. The chemical results of core samples and recently published data of surface sediments of the same project were evaluated by pollution load index (PLI), potential ecological risk index (PERI) and sediment quality guidelines (SQG). Except for Cr, all other elements in cores show lower concentrations than the SQGs confirming the high Cr contents as recorded in the most of other Sri Lankan sediments. The sediment cores indicate an unpolluted, low ecological risk sedimentary history for all core sampling locations, whereas most of the surface sediments of the lagoon are less polluted with low potential ecological risk. Present anthropogenic practices and illiteracy of this rapid developing region can damage the green environment and hence environmental management planning is suggested for a sustainable future.