Si fluxes from the continents to the ocean are a key element of the global Si cycle. Due to the ability of coastal ecosystems to process and retain Si, the ‘coastal filter’ has the potential to alter Si fluxes at a global scale. Coastal zones are diverse systems, sensitive to local environmental changes, where Si cycling is currently poorly understood. Here, we present the first palaeoenvironmental study of estuarine biogenic silica (BSi) fluxes and silicon isotope ratios in diatoms (δ30Sidiatom) using hand-picked diatom frustules in two sediment cores (CBdist and CBprox) from the Chesapeake Bay covering the last 12000 and 8000 years, respectively. Constrained by the well-understood Holocene evolution of the Chesapeake Bay, we interpret variations in Si cycling in the context of local climate, vegetation and land use changes. δ30Sidiatom varies between + 0.8 and + 1.7‰ in both sediment cores. A Si mass balance for the Chesapeake Bay suggests much higher rates of Si retention (~ 90%) within the system than seen in other coastal systems. BSi fluxes for both sediment cores co-vary with periods of sea level rise (between 9500 and 7500 a BP) and enhanced erosion due to deforestation (between 250 and 50 a BP). However, differences in δ30Sidiatom and BSi flux between the sites emphasize the importance of the seawater/freshwater mixing ratios and locally variable Si inputs from the catchment. Further, we interpret variations in δ30Sidiatom and the increase in BSi fluxes observed since European settlement (~ 250 a BP) to reflect a growing human influence on the Si cycle in the Chesapeake Bay. Thereby, land use change, especially deforestation, in the catchment is likely the major mechanism.