Mangroves play a crucial role in mitigating climate change through carbon (C) accumulation. Developing robust methods for the estimation of long-term C accumulation is essential for monitoring and reporting carbon financing projects under different global mechanisms. Moreover, understanding the effects of climate and habitat on C accumulation is important for developing mangrove management plans and conservation options. In this study, long-term above ground C accumulation in the three most dominated mangrove tree species, Heritiera fomes, Excoecaria agallocha and Sonneratia apetala, was estimated using a dendrochronological approach in two contrasting (low vs high) salinity zones in the Bangladesh Sundarbans. In addition, how climate and habitat (e.g., regulators and soil resources) influence C accumulation was analyzed. For the first time, we estimated C accumulation in mangrove species over their entire lifetime using stem disc-derived tree-ring data. The C accumulation patterns exhibited similar patterns of variation, increasing from pith to bark in each case. C accumulation was significantly higher in the low salinity zone (LSZ) than in the high salinity zone (HSZ) (p < 0.05). The cumulative C accumulation increased with tree age in each case, and C accumulation was influenced mainly by seasonal precipitation, especially during monsoon. General additive modeling (GAM) revealed that soil salinity had a stronger effect on C accumulation variability in the studied tree species. Other regulatory variables (i.e., siltation and elevation) and soil resources (i.e., P and K) had species-specific influences on C accumulation. Tree-ring data show the potential to yield better biomass and C estimations, which could aid frequent and rapid reporting of C accumulation in mangroves. Moreover, the results also suggest that climate and regulatory variables, especially soil salinity, together impact the C cycles in the Sundarbans.