The primary objective of this study is to determine trace metal contamination in environmental samples obtained from Pahang River and Kelantan River, Malaysia which may help to identify the risk of sustainable dredging in these areas. This research also proceeds to compare the trace metal concentration with the National Water Quality Standards of Malaysia, Interim Canadian Sediment Quality Guidelines and Malaysian Food Act 1983 to determine its limits and risks. Samples of water, sediment, snails and fishes were collected and analyzed for As, Cu, Cd, Cr, Fe, Pb, Ni, Mn, and Hg by using atomic absorption spectrophotometer. It was found that the concentration of trace metals namely As, Cu, Cd, Cr, Pb, Ni, and Hg in river water, sediment, snail and fish samples in Pahang River were lower than the maximum allowable limits, except for Fe and Mn. In Kelantan River, the concentration of trace metals indicating that it is contaminated with Fe, Mn, Pb, Cr, Cu, Hg, and As as all trace metals exceeded the maximum allowable limits. Negative impacts may arise, and the river may contaminate more in future if there is no proper management to tackle this issue during execution of dredging activities.