Mercury (Hg) re-emission from sediment is an important process in the biogeochemistry cycles of Hg in the aquatic ecosystem. The contribution of Hg released from sediment to water remains unclear for some shallow lakes. Lake Nansi is a typical shallow lake in northern China that is divided into upper and lower lakes by a dam. The Hg species in the water profile and sediment were measured from two sampling sites in the lake. Nansi Lake was not markedly contaminated by Hg. The Hg profile in the sediment indicated that the demand for energy and the policy management in the catchment influenced the Hg accumulation in its sediment. On the basis of Fick's first law and the sedimentation rate, the diffusion flux of dissolved Hg from sediment to overlying water and the accumulation flux were estimated. According to one-year scale estimation, approximately 10%-13% the Hg in the sediments can be re-released into the overlying water. The Hg diffused from the sediment accounted for 7.9%-16% of the Hg in the overlying water. These results of this study improve the understanding of the sources of pollution in water and enable researchers to focus on the contribution of sediment to the pollution of water in shallow lakes.