Biogeochemical silicon (Si) cycling in coastal systems is highly influenced by anthropogenic perturbations in recent decades. Here, we present a systematic study on the distribution of stable Si isotopes of dissolved silicate (δ30SiDSi) in a highly eutrophic coastal system, the Baltic Sea. Besides the well‐known processes, diatom production and dissolution regulating δ30SiDSi values in the water column, we combined field data with a box model to examine the role of human disturbances on Si cycling in the Baltic Sea. Results reveal that (1) damming led to increased δ30SiDSi values in water but had little impacts on their vertical distribution; (2) decrease in saltwater inflow due to enhanced thermal stratification had negligible impacts on the δ30SiDSi distribution. An atypical vertical distribution of δ30SiDSi with higher values in deep water (1.57–1.95‰) relative to those in surface water (1.24–1.68‰) was observed in the central basin. Model results suggest the role of enhanced biogenic silica (BSi) deposition and subsequently regenerated dissolved silicate (DSi) flux from sediments. Specifically, eutrophication enhances diatom production, resulting in elevated exports of highly fractionated BSi to deep water and sediments. In situ sedimentary geochemical processes, such as authigenic clay formation, further fractionate Si isotopes and increase pore‐water δ30SiDSi values, which then leads to pore‐water DSi flux carrying higher δ30SiDSi compositions into deep water. Our findings provide new quantitative information on how the isotope‐based Si cycle responds to human perturbations in coastal seas and shed lights on shifts of Si export to open ocean.