Based on the water quality monitoring data of 8 main estuary sections in Guangdong, Hong Kong and Macao Great Bay Area(GBA)from 2015 to 2019, 5 conventional water quality indexes of BOD₅, NH₃-N, COD, TP, TN and 6 heavy metal indexes of Hg, Pb, Cu, Zn, Cr⁶⁺ and Cd are selected. According to GB 3838—2002 , the pollution index method and seasonal Kendall test method were applied, and the water quality evaluation and change trend analysis of estuaries in the GBA were carried out. The results show that the pollution type of the estuary in the GBA is mainly nitrogen and phosphorus pollution, and the main pollutant is TN. The pollution degree of the estuary in the Dongjiang River Basin is greater than that in the Northwest River Delta Basin. Organic pollution and heavy metal pollution are relatively light, and the pollution index of heavy metal Hg shows a rapid upward trend in 2019. From 2015 to 2019, the concentration of water quality index BOD₅ in the GBA decreased most significantly, NH₃-N and COD decreased significantly, and TP and TN pollution did not improve. The pollution of Dongjiang River Basin is improving, and that of Northwest River Delta is aggravating.