Mercury (Hg) isotopes provide a useful tool to understand Hg sources and processes in the environment. The Hg isotopic composition of seawater remains poorly constrained due to the lack of an efficient method to process large volumes of low-Hg-concentration seawater samples. Here, we develop a continuous flow–double purge and trap device for the in situ preconcentration of Hg in seawater. This method yielded a good Hg recovery of 91.7 ± 3.3% (n = 4, 1SD) for spiked seawater samples and gave reasonably similar Hg isotope ratios of NIST 8610, indicating a limited matrix effect and limited Hg isotope fractionation during processing of seawater. NIST 8610 δ²⁰²Hg (−0.55 ± 0.09‰, n = 4, 1SD) and Δ¹⁹⁹Hg (0.07 ± 0.02‰, n = 4, 1SD) were similar to previously published data. The method was successfully applied to seawater collected from the Xiamen Bay and the South China Sea. The seawater samples showed a Hg recovery of 91.6 ± 5.4% (n = 12, 1SD). Seawater Δ¹⁹⁹Hg (−0.04 ± 0.05‰, n = 7, 1SD) in the Xiamen Bay was different from seawater Δ¹⁹⁹Hg (0.05 ± 0.07‰, n = 5, 1SD) in the South China Sea, which implies distinct Hg sources to coastal and open ocean areas and highlights the robustness of our method in understanding the Hg isotopic composition of seawater.