The Water Sediment Regulation Scheme (WSRS) is a unique engineering measure that has been regularly performed to reduce reservoir sedimentation and increase the flood capacity of the Yellow River in China since 2002. As a side effect, the WSRS greatly increases the monthly input flux of nutrients to the Bohai Sea (BHS) in summer, potentially exacerbating eutrophication levels therein and subsequently affecting the growth of phytoplankton. However, its influence on the Chlorophyll-a (Chl-a) dynamics over the BHS is still poorly understood. In this study, two approaches were adopted to investigate it: 1) long-term in-situ observations and satellite-derived data of surface Chl-a were used to study its seasonal variations before and since 2002, and 2) one 1D physical-biological coupled model was developed to evaluate the impact of WSRS on seasonal Chl-a. The results showed that the surface Chl-a exhibited two peaks in spring and autumn until 2002, but has exhibited only one peak in spring-summer since 2002. Satellite-derived Chl-a concentrations in spring-summer since 2002 have increased by 56% compared to those until 2002. The simulated results showed that the change in Yellow River discharge induced by the WSRS has resulted in the appearance of high concentrations of Chl-a in summer over the Central Bohai Sea since 2002. The WSRS increased the ratio of added Chl-a owing to the riverine nutrients to total Chl-a by 19% compared to that until 2002. Overall, WSRS greatly affects the seasonal cycling of Chl-a in the Bohai Sea, and the side effect needs to be considered.