To study the response process of peak water level of the Pearl River Delta on the river-bed deepening due to sandmining, the harmonic analysis is used to remove the influence of nodal modulated fluctuation of tide in water level time series, and a method called the probability density function is adopted to explore the evolution trend of water levels in the delta. The results show that the peak water level decreases significantly after the channel deepening in the upstream regions. In the transition regions, the peak water level rises. In the tide-dominated regions or downstream region, changes of peak water level should be related to the sea level rise or other human activities.