[Objective] The study aimed to predict the peak water level in Pearl River Estuary under the background of sea level rise. [Method] The changing trends of peak water level at Denglongshan station and Hengmen station were analyzed firstly on the basis of regression models, and then sea level rise in Pearl River Estuary in 2050 was predicted to estimate the 1-in-50-year peak water level in the same year. [Result] Regression analyses showed that the increasing rate of peak water level over past years was 6.3 mm/a at Denglongshan station and 5.8 mm/a at Hengmen station. In addition, if sea level will rise by 20, 30 and 60 cm respectively in 2050, it was predicted that the 1-in-50-year peak water level will reach 3.04, 3.14 and 3.44 m at Denglongshan station, and 3.19, 3.29 and 3.59 m at Hengmen station separately. [Conclusion] The estimation of peak water level in Pearl River Estuary could provide theoretical references for water resources planning.