Arsenic (As) and mercury (Hg) are pollutants presented in marine environment. A process of atomic fluorescence spectrometry was proposed for the simultaneous determination of As and Hg in marine sediment samples (n = 38) collected from the Changjiang River Estuary and adjacent East China Sea. The proposed method used an optimized pretreatment procedure in an aqua regia–H2O digestion system. Recoveries of As and Hg increased to 97％ and 98％, respectively, with suitable precisions (2.7％–4.1％) under optimized process conditions. As and Hg were widely presented in these samples, with the ranges of content values were 2.39–8.77 μg/g for As and 48.03–410.8 ng/g for Hg. Results indicate that anthropogenic factors strongly influence the abundances of As and Hg in investigated samples. The preliminary environmental risk assessment was investigated using the geoaccumulation index (Igeo) and anthropogenic contribution rate (M). Findings reveal that Hg demonstrates a strong ecological risk (with average values of 1.3 and 72％ for Igeo and M, respectively) in the sediments from the Changjiang River Estuary and adjacent East China Sea. Therefore, Hg should be considered in future investigations.