Mangrove forests are important wetland ecosystems that are a sink for mercury from tides, rivers and precipitation, and can also be sources of mercury production and export. Natural abundance mercury stable isotope ratios have been proven to be a useful tool to investigate mercury behavior in various ecosystems. In this study, mercury isotopic data were collected from seawater, sediments, air, and plant tissues in two mangrove forests in Guangxi and Fujian provinces, China, to study the transport and transformation of mercury in mangrove sediments. The mangroves were primarily subject to mercury inputs from external sources, such as anthropogenic activities, atmospheric deposition, and the surrounding seawater. An isotope mixing model based on mass independent fractionation (MIF) estimated that the mangrove wetland ecosystems accounted for <40% of the mercury in the surrounding seawater. The mercury in plant root tissues was derived mainly from sediments and enriched with light mercury isotopes. The exogenous mercury inputs from the fallen leaves were diluted by seawater, leading to a positive ΔHg offset between the fallen leaves and sediments. Unlike river and lake ecosystems, mangrove ecosystems are affected by tidal action, and the δHg and ΔHg values of sediments were more negative than that of the surrounding seawater. The isotopic signature differences between these environmental samples were partially due to isotope fractionation driven by various physical and chemical processes (e.g., sorption, photoreduction, deposition, and absorption). These results contribute to a better understanding of the biogeochemical cycling of mercury in mangrove wetland ecosystems.