Salt marshes in New York City’s Jamaica Bay have been disappearing and deteriorating since early 1900s, resulting in the loss of long-term accumulated carbon storage. However, the spatial variations and mechanisms in vertical accretion and soil organic carbon (SOC) sequestration across this highly urbanized estuary remains unclear. In this study, we collected soil cores to a depth of ~ 50 cm across Jamaica Bay to study the spatial variability in long-term (50–100 years) vertical accretion, the accumulation of mineral sediment and organic matter, and SOC sequestration. Results of gamma spectrometry analysis of ¹³⁷Cs and ²¹⁰Pb show that there was moderate spatial variability in long-term vertical accretion rates across Jamaica Bay study sites (mean: 0.48 ± 0.13 cm yr^− 1, range: 0.36–0.78 cm yr^− 1). This local scale spatial variability in vertical accretion is largely driven by spatial variations of sedimentation. The magnitude of the long-term vertical accretion in Jamaica Bay is significantly correlated with organic matter accumulation, but not with mineral sediment. However, the role of organic matter in contributing to vertical accretion has been declining. The declining role of organic matter to vertical accretion is reflected by the lower SOC sequestration rate (mean: 128 and range: 26–189 g C m^− 2 yr^− 1 using the ²¹⁰Pb dating technique) compared to the global mean salt marsh SOC sequestration rate (244 g C m^− 2 yr^− 1). This is especially so on the marsh islands in the degrading western part of the bay where SOC sequestration was less than half the global average.