Freshwater marshes are prevalent and important stores of carbon. They bury carbon in deeper soils, although reported rates of carbon accumulation are significantly higher over recent (decadal) versus longer (centennial and millennial) timescales. Intrinsic organic matter degradation, long-term climatic and ecological changes, and recent anthropogenic impacts on sediment fluxes and organic matter production may have a role in explaining this discrepancy, yet remain poorly understood for freshwater marshes. We collected a 4-m core from a riverine-influenced marsh in the watershed of Big Creek which drains into Lake Erie in southern Ontario, Canada, and conducted radiometric dating, elemental analyses, and programmed pyrolysis for organic matter characterization. Over the past 5,710 calibrated years, burial of organic (on average 26 ± 34 g C m-2 yr-1) and inorganic (22 ± 25 g C m-2 yr-1) carbon fractions has resulted in high rates of carbon accumulation. We found that elevated recent rates of organic carbon accumulation are driven by fractions that have low thermal stability and are predominantly from aquatic sources. This type of organic carbon is buried intermittently in deeper marsh sediments and corresponds to major hydro-fluvial events (e.g., Nipissing highstands), which coincide with regional marsh development. We deduce that lower fractions of labile carbon in deeper soils reflect long-term degradation, which underscores the notion that high recent rates of carbon accumulation are generally not sustained over centuries and millennia. Our research demonstrates the importance of identifying various carbon fractions in understanding carbon burial in freshwater marsh soils, and informing marsh conservation.