Intensive human activity has caused significant changes in the river morphology and hydrological characteristics of the Pearl River Delta. Particularly, in‐channel mining and dam construction have induced remarkable levels of downward riverbed incision. Although strict control measures have been implemented for in‐channel sand mining, it remains unclear how the river has evolved since the abandonment of high‐intensity mining and its impact on flow diversion at the downstream confluence. This study presents the hydrological and morphological adjustments in the lower Beijiang River, the second largest tributary of the Pearl River, under the impacts of human interventions. A hydrodynamic model was developed to reveal the impacts of riverbed deformation on the flow diversion ratio at Sixianjiao, the confluence of the Beijaing River and the Xijiang River. The results showed that construction of cascade reservoirs upstream reach did not strongly influence run‐off, whereas incoming sediment loads were decreased. Because of upstream damming and in‐channel sand mining, a dramatic downward incision was observed in the lower Beijiang River, with a degradation volume of approximately 239.8 million m3 from 1999 to 2012. Particularly, in the upper reach, the incision depth was typically larger than 8 m. Riverbed incision caused continuous changes in the water stage–discharge relationship, and discharge increased remarkably under the same water level at the three hydrometric stations. During 2012–2020, because in‐channel sand mining was strictly controlled, rapid degradation was alleviated, deposition occurred in some cross‐sections and the deformation volume decreased by approximately 90% compared to that in the last period. A fast downward incision induced a change in flow exchange between the two rivers, and the flow diversion ratio of the Beijiang River increased from an average of 17% before 1998 to more than 21%.