Anoxic conditions, occurring in enclosed water bodies from an overabundance of organic matter, cause further deterioration of the aquatic environment through nutrient elution and hydrogen sulfide production. The quantises of biochemical reactions under anaerobic states, such as denitnfication, iron reduction and sulfate reduction are important research topics when considering conservation and improvement of water quality environment. This study involved regular observations for two years in the reservoir, in which overabundant organic matter was prominent due to humic acid, to evaluate the water quality dynamic near the bottom during long-term anoxic periods. Based on the temporal changes of dissolved oxygen, nitrate-nitrogen, ammonia-nitrogen, phosphate-phosphorus, sulfide, total iron ions, and sulfate, this study focused specifically on the influence of the redox state of the sediment surface during the early stage of thermal stratification on the anaerobic biochemical reactions. As a result, nitrate-nitrogen started to decrease to zero due to denitnfication as soon as the anoxic state occurred, and then both ammonia-nitrogen and phosphate-phosphorus increased linearly with time due to iron reduction after nitrate-nitrogen had decreased to zero. Sulfide began to increase linearly due to sulfate reduction as soon as nitrate-nitrogen disappeared. Also, the initial redox state of sediment impacted on the change characteristics of phosphate-phosphorus, ammonia-nitrogen and sulfide in the points of increasing timings, duration, and rates. It was concluded that our results would provide important finding about the mechanisms of aqueous environmental deterioration due to organic pollution as well as beneficial information for the modification of water quality prediction model.