To study how the biogeochemical Si cycle in large river estuary and coastal areas has responded to one of the largest river regulation projects in the world, we conducted four cruises covering 33 stations across the Yellow River estuary and Bohai Sea via the RV CHUANGXINYI over four seasons, from October 2021 to August 2022. Temperature and salinity were monitored by a SeaBird-911 Conductivity-Temperature-Depth (CTD) recorder. Nutrients of phosphate, dissolved inorganic nitrogen and dissolved silica were measured by SEAL QuAAtro 39-SFA analyzer, biogenic silica was measured by alkaline digestion method, and Si isotope values of dissolved silica isotopes were measured by MC-ICP-MS. Our data reveal that the Si cycle in the Yellow River estuary and Bohai Sea is subject to high pressure of human activities and large natural variability.