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The San Francisco Bay has the largest concentration of salt marshes in the state of California. In the last 170 years, the vast majority of the historic tidal wetlands in the Bay have been significantly altered or destroyed due to diking, filling and other processes. Many of the remaining marshes have been impacted by changing sedimentation regimes and related loadings of pollutants such as heavy metals (Sr, Al, Fe, Ti, Cu, Pb, Ni, Zn) over this period, making ecological trajectories and resilience to disturbance uncertain. Here we examine changing sediment accretion rates, coupled with the longest and highest resolution heavy metal accumulation data from three San Francisco Bay marshes, to examine European impacts in the context of earlier Holocene variability. The results are consistent with larger-scale analyses and indicate that European alterations of landscapes and shorelines had geographically variable impacts on marsh sediment accumulation. Despite differential impacts on net sediment accretion, initial European impacts appear to have decreased the proportion of organic material in the marsh sediments, likely due to the delivery of eroded inorganic sediment from landscapes and shorelines. The results confirm significant European impacts on the geochemistry of marshes in the San Francisco Bay over the last ~150–200 years. Post-European arrival levels of Pb are unprecedented throughout the earlier Holocene. However, these values have declined in recent years. Concentrations of Sr, Ti, Cu, Ni, and Zn also increased following European arrival. Our results show that post-European concentrations are not so far removed compared to pre-European maximum concentrations. As sedimentation regimes and emissions of Pb and delivery of other metals have decreased, and as organic productivity increased on the marshes, environmental trajectories are shifting back towards their immediate pre-European conditions. [ABSTRACT FROM AUTHOR]