The risk factor of the receiving water body is one of the important factors that affect the self-purification ability of the water body. Analyzing the concentration and removal rate of the target substances such as suspended solid (SS), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) in the receiving water body during the life cycle can trace the risk factor. Based on this, this article takes a sewage treatment plant and its receiving water body in Nanjing as the research object, sets up five sampling points, and calculates the target concentration and removal rate using the cellular automata-Markov chain Monte Carlo method. Thus, risk assessment of water bodies can be achieved. The results show that: (1) the concentration of the target substance in each process stage has obviously decreased during the life cycle, with an average concentration of 3–18 mg/L; (2) in the life cycle, the highest removal rate of target concentration in each process section can reach 85%; (3) the concentration of target substances SS, COD, TN, TN, TP, and TP at the outlet of the sewage treatment plant is relatively high. Practice has proven that this research method can assess the risk factors of receiving water bodies, so as to improve the scientific, refined and standardized environmental management.