The estuarine environment can serve as either a source or sink of carbon relative to the coastal ocean carbon budget. A variety of time-dependent processes such as sedimentation, carbon supply, and productivity dictate how estuarine systems operate, and Mobile Bay is a system that has experienced both natural and anthropogenic perturbations that influenced depositional processes and carbon cycling. Sediments from eight box cores provide a record of change in bulk sediment accumulation and carbon burial over the past 110 years. Accumulation rates in the central part of the basin (0.09 g cm−2) were 60–80 % less than those observed at the head (0.361 g cm−2) and mouth (0.564 g cm−2) of the bay. Sediment accumulation in the central bay decreased during the past 90 years in response to both anthropogenic (causeway construction) and natural (tropical cyclones) perturbations. Sediment accumulation inevitably increased the residence time of organic carbon in the oxic zone, as observed in modeled remineralization rates, and reduced the overall carbon burial. Such observations highlight the critical balance among sediment accumulation, carbon remineralization, and carbon burial in dynamic coastal environments. Time-series analysis based solely on short-term observation would not capture the long-term effects of changes in sedimentation on carbon cycling. Identifying these relationships over longer timescales (multi-annual to decadal) will provide a far better evaluation of coastal ocean carbon budgets.