Estuaries play a critical role in exchanging of energy and materials between land and ocean. To better understand biogeochemical cycle flux of mercury, it’s important to reveal the migration pattern of mercury and related influencing factors. Porewater samples were collected from the Jiulong River estuary during the dry and wet seasons. The total mercury (THg) concentrations and mercury isotopic compositions of surface water and sediment were also analyzed as well as their relationships with salinity, respectively. The results showed that THg concentrations of porewater[(38.28±26.80)ng·L-1
]was generally higher than of surface water[(9.81±10.21)ng·L-1
], but the THg concentration of porewater at some stations was lower than that of surface water during the cruise impacted by heavy rain, indicating that influence of precipitation events on mercury migration in this estuary; mercury isotope composition of porewater also indicated that mercury in the estuary may migrate along the direction of surface water-pore water-sediment during the mixing process of seawater and freshwater. During the mixing process of seawater and freshwater, the additional mercury was added to the surface water in the wet season (Hg addition pattern) and mercury was additionally removed from the surface water (Hg removal pattern) in the dry season, which was related to the resuspension and flocculation of suspended particulate matters. In addition, the Hg addition pattern was more intense when the current converged at the shallow part of the channel in the mid estuary compared to when the seawater has already flooded into the whole estuary. The relationship between the mercury isotopic composition and salinity suggested that the δ202
Hg and Δ199
Hg values of surface water increased during the mixing process in the wet and dry seasons when there was no occasional precipitation event, indicating that the Hg removal or addition pattern may not directly cause the change of mercury isotopic composition in surface water. However, the δ202
Hg values of surface water decreased and Δ199
Hg values remained unchanged in the dry season affected by occasional precipitation events, suggesting that precipitation events had an effect on the mercury migration in the estuary.