From 2004 to 2019, human activities have caused a profound and irreversible impact on Qinzhou Bay (QZB) through large-scale land reclamation and land-based sewage discharge. In this study, based on the satellite images and marine charts, a hydro-biogeochemical model was established to analyze the cumulative effect of human activities on water quality in Qinzhou Bay during the past decades. Under the double anthropogenic pressures, the concentration of chemical oxygen demand (COD) in QZB has slightly decreased from 0.976 mg/L to 0.909 mg/L. But the concentration of inorganic nitrogen (DIN) and inorganic phosphorus (DIP) increased obviously from 0.146 mg/L and 0.023 mg/L to 0.230 mg/L and 0.027 mg/L, respectively. The statistical results show that the area of heavily polluted and severe eutrophication water has increased dramatically, indicating the water quality in QZB being degenerated. According to the characteristics of pollution discharge in the bay, the share rate method was used to calculate the environment capacity in different scenarios. The results show that the actual emissions far exceed the maximum allowed amount in the bay, particularly in Maoling River and Qinjiang River, where the emissions of pollutants need to be reduced urgently. Because of the decrease of the water area and water exchange capacity caused by land reclamation, the environment capacity has reduced compare to the historical situation. The calculation of sewage discharge optimization method for Maowei Sea indicates that Maoling River should share more sewage discharge than Qinjiang River, which is conducive to the improvement of water quality in Maowei Sea. It is estimated that the environmental capacity value loss of Qinzhou Bay caused by two anthropogenic pressures is approximate 2.695 billion per year, so compensation should be considered before exploitation and utilization of the coastal ocean.