Residual water level (i.e. the tidally averaged water level) is mainly driven by the residual frictional effect and strongly related to the nonlinear tide-river interactions. Understanding its development and evolution is important with regard to sustainable water resources management in general, such as flood control and salt intrusion. In recent decades, due to the intensive human interventions the patterns of tide-river dynamic and the corresponding residual water level in the Modaomen Estuary of the Pearl River have changed a lot. In this study, a nonstationary harmonic model (NS_TIDE) was used to reproduce the natural dynamics residual water level that would have occurred in absence of the large-scale human interventions (such as sand excavation) based on collected observed hydrological data from 5 stations in the Modaomen Estuary spanning the period 1958–2015. Model results show that, under the overall influence of human interventions, the amplitudes of the K₁ and M₂ constituents in 1994 and 2003 were increased significantly, with the maximum increase by 0.13 m and 0.09 m, respectively. It was shown that the residual water level along the Modaomen estuary was significantly decreased, with the maximum decrease by 1.39 m in Makou station. Moreover, we showed that the decline of residual water level during the flood season was much greater than that during the dry season, and the more upstream the location of the station, the more obvious of the change is. The underlying mechanism can be primarily attributed to reduction of the residual water level slope due to the deepening of the channels along the Modaomen estuary caused by human interventions.