Development and urbanization processes around Terengganu River estuary are expected to release a significant amount of heavy metals into the existing bottom sediment. However, information on how and why these metals are attached into specific fraction of sediments is still lacking. Therefore, this study aimed to explain the heavy metal concentration distribution in each available fraction at Terengganu River estuary. In this study, nine surface sediments originated from various human activities area in Terengganu River estuary were collected during four different sampling sessions in 2017. Heavy metal content from the collected sediments were extracted using 3-steps BCR sequential extraction method followed by detection using Inductively Coupled Plasma Mass-Spectrometer (ICP-MS) and we discovered that the total concentration of Arsenic (As), Cobalt (Co), Copper (Cu), and Zinc (Zn) ranged from 2.18 to 17.48 mg/kg dry wt., 2.53 to 20.53 mg/kg dry wt., 1.01 to 13.13 mg/kg dry wt., and 6.10 to 65.71 mg/kg dry wt., respectively. Dominance of metals in each fraction can be arranged as follows: As: residual > reducible > exchangeable > oxidizable; Co: residual > exchangeable > reducible > oxidizable; Cu: residual > oxidizable > reducible > exchangeable; Zn: residual > exchangeable > reducible > oxidizable. Availability of metals in sediment at Terengganu River estuary is limited since that majority of metals resides in non-mobilisable fraction of the sediment. In essence, sequential extraction provides information regarding the metals’ fractionation, availability and mobility, which could be used in assessing the environmental contamination in the area.