To study the characteristics of water quality variation in the Pearl River Estuary during the recent years, the water quality in the Pearl River Estuary is evaluated and the tempo-spatial distribution characteristics of water quality is analyzed, based on data from 51 monthly collected water quality sampling points from 2018 to 2020, with evaluation indices filtered using principal factor analysis and improvement on traditional comprehensive water quality identification index method using combinatorial integration method.Results show that the comprehensive water quality identification index method combined with combinatorial integration method takes both excessive pollutants index and other indices into account, so as to obtain reasonable and reliable results, which means the method is suitable for large-scale watershed water quality assessment. The water qualities in all drainages tend to improve over the years, mainly from class of inferior Ⅴ to Ⅲ, which met the water quality goals in water environment function zones. The water quality in the western regions was slightly worse than that in the eastern regions.The river water quality in the Nanshan district was better than that in the Dakonggang district, however the improvement in river water quality in Dakonggang and Qianhai district was more significant. The water quality of the upstream was generally better than that of the downstream. Estuary water quality fluctuates greatly with the seasons, which was generally affected by sea water pollution and the tidal sluice operations.