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Mangrove ecosystems represent low-cost climate-regulating systems through carbon storage in their sediments. However, considering the complex shifts in shallow coastal ecosystems, it is clear from just a few sets of environmental impacts on their carbon storage that there is a deficit in the information required for preserving this service. Here, we investigated the spatial and temporal variability of hydrographic factors (water temperature, pH, salinity, dissolved oxygen (DO), flow velocity, turbidity) and sediment characteristics (sedimentation rate and sediment grain size) on the intricate carbon dynamics of mangroves by examining which key variable(s) control mangrove sediment organic matter (OM). We used in-situ monitoring to assess the hydrographic dynamics, sedimentation rate, sediment organic content, and granulometry. Laboratory loss-on-ignition and granulometric methods were employed to quantify OM in trapped and bottom sediments and sediment grain size, respectively. Based on the findings, water pH, salinity, and DO were the key regulators of OM in sediments. Despite conventional expectations, the study observed positive effects of DO on OM, highlighting the possible role of aquatic plant photosynthesis and freshwater inflow. Sedimentation rates, usually considered crucial for OM accumulation, showed no significant relationship, emphasizing the importance of sediment content over quantity. Noteworthy findings include the role of sediment grain size in OM storage within mangrove sediments. Even though the grain size class of 63 μm diameter had the highest mean weight across the studied sites, there were significant positive correlations between Trap and Bottom OM with 500 and 2000 μm grain size classes, emphasizing the need to consider sediment characteristics in carbon dynamics assessments. Overall, this research provides valuable insights into the intricate environmental dynamics of mangrove ecosystems that are crucial to understanding and managing these vital coastal habitats., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)