Wuliangsuhai Lake, as a typical shallow lake in Hetao irrigation district, locates in China Northern. We took sediment samples in spring, summer, autumn, and winter, respectively. The total arsenic (As), total mercury (Hg) and other parameters (temperature, pH, EC, particle size of sediments and Organic matter in sediments) were measured. Based on the temporal variations, seasonal comparisons and factor analysis, the following conclusions were obtained: (1) the seasonal characteristics of Hg and As were: summer > spring > autumn > winter, and spring > summer > autumn > winter. (2) The higher concentration of Hg and As during summer was considered to be caused by the higher organic matter and humus content, which made heavy metals strongly adsorbed and complexed, and changes of the organic matter content would enhance the binding state of the less active organic matter then deposit in sediment. (3) The speciation of mercury and arsenic was also the reason, in summer, the Hg0 in atmosphere was oxidized to Hg2+, entered into water through rainwater washing and dry deposition, then, soluble Hg2+ was quickly adsorbed and fixed in sediment, a series of transformations reduces its activity. The As3+ would be oxidized to As5+ which would form precipitated. Therefore, the content of Hg and As, environmental risk and potential ecological risk of mercury in sediments were higher in summer.