Downcore variation of trace metals in sediment cores along the coastal line is one of the markers to assess the intrusion of industrial pollutants into the aquatic environment. Fifty sediment core samples from the Mumbai Harbour Bay (MHB), were studied for the trace element content. MHB is a recipient of effluents from different industries situated all along its coast around Thane–Belapur region. The average concentrations of Titanium (Ti), Manganese (Mn), Iron (Fe), Nickel (Ni), Copper (Cu), Zinc (Zn) were determined by inductively coupled plasma-optical emission spectroscopy and complemented by analysing with energy dispersive X-ray fluorescence spectrometry. In addition to this, depth profiles of K and Ca were also studied to assess the homogeneity of the geological strata of the region. Trace metals such as Cu, Ni and Zn show enrichment between 16 to 28 cm, whereas, uniform distribution through out the core was observed for K, Ca, Ti, Mn and Fe. Chronology of the heavy metal deposition was predicated based on the average sedimentation rate (0.92 ± 0.08 cm year−1) derived using depth-wise 137Cs concentration profile in core of bottom sediment. The results of the analysis showed that MHB had received excess inputs of Cu, Ni and Zn in the year 1981, 1988 and 1982, respectively. Surface concentration of Cu, Ni, Zn and Fe compared to the reference site indicates moderate pollution in the recent years whereas for elements K, Ca, Ti and Mn, the values are normal indicating MHB unpolluted for the latter elements.