Potentially toxic elements (PTEs) have attracted substantial attention because of their widespread sources, long residue time and easy accumulation. PTEs in the surface sediments of inshore waters are strongly affected by human activities because these waters are a zone of interaction between the ocean and land. In the present study, to explore the environmental geochemical behaviour and source of PTEs in the surface sediments of coastal waters, the contents and spatial distributions of copper (Cu), lead (Pb), zinc (Zn), cadmium (Cd), chromium (Cr), mercury (Hg) and arsenic (As) in different regions of Xiamen Bay were investigated. The data were processed by multivariate statistical methods, and the distribution characteristics of PTEs in the surface sediments of Xiamen Bay were analysed. In addition, the pollution load index (PLI), geo-accumulation index (Igeo) and potential ecological index(RI) were used to evaluate the pollution degree and potential risk in the surface sediments of Xiamen Bay, and the positive matrix factorisation (PMF) model was used to analyse the source. The results show that Zn had the highest mean concentration, followed by Pb, Cr, Cu, As, Cd and Hg, among the seven PTEs. The mean contents of Pb, Zn, Cd, Cu and Hg, and especially Hg and Cd, were higher than the corresponding environmental background values. The average PLI value indicated that the Xiamen Bay sediment was moderately contaminated by PTEs. The Igeo results showed that Xiamen Bay was moderately to strongly polluted by Cd and Hg. The proportions of samples with low, medium and strong risk levels were 11.63%, 74.42%, and 13.95% in surface sediments, respectively. PMF models showed that the input of chemical fertilizer and medication, anthropogenic atmospheric components and terrestrial detritus were the main sources of PTEs in the surface sediment of Xiamen Bay.