In coastal landfill facilities that are constructed to contain municipal and industrial wastes in Japan, natural marine clay layers serve as bottom liners to prevent pollutant migration. Leachates from landfills are rich in dissolved organic carbon (DOC) that can be used by micro-organisms. Biological processes could lead to redox reactions that change the pH and Eh. These biochemical factors may strongly influence the behavior of pollutants leached from landfills, particularly heavy metals. In this paper, modified batch tests were conducted to investigate the effects of pH and Eh and to simulate both chemical and biochemical reactions on zinc mobility in a marine clay layer. To examine the effects of pH and Eh, the pH and Eh were controlled by adding acid or base, respectively, and a reducing agent. To study the zinc mobility, biochemical reactions were enhanced by cultivating native micro-organisms, which gradually changed the pH and Eh conditions. Batch tests with different DOC concentrations were also conducted to evaluate the effect of DOC on zinc mobility. In addition, biochemical processes in the bottom clay liners at coastal landfill sites that receive municipal solid waste (MSW) incinerator ash were simulated by batch tests using a solution of MSW incinerator ash mixed with seawater along with cultivating native micro-organisms found in marine clay. The experimental results indicated that microbial activities in closed soil-water systems result in strongly reduced conditions compared to that controlled by a strong reducing agent, and that the zinc mobility is lowered through the formation of sulfides. Although microbial activity was initially limited under highly alkaline conditions due to MSW incinerator ash, the pH gradually decreased mainly due to the formation of organic acids from microbial activity. Under the oxidized conditions, the solubility of zinc was controlled by pH and the Eh had a negligible effect on the zinc concentration. DOC in the leachate served as a bioavailable carbon source for microbial activities, which promoted anaerobic conditions in the soil-water system and the immobilization of zinc. However, DOC also formed soluble complexes with heavy metals, which increased the zinc concentration. These observations confirmed that heavy metals in the leachates became immobilized under the conditions found at landfill bottom liners when estimated in terms of pH, Eh, and DOC.