The San Juan Bay Estuary, Puerto Rico, contains mangrove forests that store significant amounts of organic carbon in soils and biomass. There is a strong urbanization gradient across the estuary, from the highly urbanized and clogged Caño Martin Peña in the western part of the estuary, a series of lagoons in the center of the estuary, and a tropical forest reserve (Piñones) in the easternmost part with limited urbanization. We collected sediment cores to determine carbon burial rates and vertical sediment accretion from five sites in the San Juan Bay Estuary. Cores were radiometrically-dated using lead-210 and the Plum age model. Sites had soil C burial rates ranging from 50 grams per meter squared per year (g m-2 y-1) in the San José lagoon to 632 g m-2 y-1 in the Caño Martin Peña in recent decades. Soil accretion and carbon burial rates were greater in recent decades (1970-2016) compared to historic decades (1930-1970) at some of the forest mangrove sites (i.e. Caño Martin Peña). Apparently, not only urbanization, but site-specific flushing patterns, landscape setting, and soil characteristics affected soil C burial rates. This dataset can help evaluate how differences in urbanization (low in the forest preserve to high in the clogged canal), flushing, and landscape setting influence soil accretion and carbon burial in urban, tropical mangrove forests.