A mechanistic mangrove ecosystem model for evaluating carbon absorption, fixation, and storage functions across daily to seasonal timescales

• A mangrove model simulating C fluxes from daily to seasonal scales was developed. • Tidal cycles, benthic–pelagic coupling, and mangrove physiology are in the model. • Carbon absorption and fixation increased in spring and summer via photosynthesis. • Residual ponding enhances DIC and TA via mineralization and CaCO₃ dissolution. • Mangroves enhanced carbon absorption, fixation, and storage by 9 ×, 3 ×, and 6 ×. Mangrove ecosystems function as important carbon sinks; however, accurately quantifying their carbon dynamics remains challenging because of the complex interplay of tidal fluctuations, sediment–water interface interactions, and biogeochemical cycling. Many existing models lack the temporal resolution and mechanistic precision necessary to adequately capture these dynamic processes, particularly in intertidal environments. To address this issue, we developed a mangrove ecosystem model [EMAGIN-B.C_MG] by incorporating mangrove physiology and tidal hydrodynamics into the EMAGIN-B.C. model, which represents benthic–pelagic coupled ecosystems, including phytoplankton, benthic algae, zooplankton, benthic fauna, detritus, and nutrients, through biological, chemical, and physical processes. Model validation was conducted by comparing the results with time series observations of dissolved inorganic carbon (DIC), total alkalinity (TA), and dissolved oxygen, as well as annual carbon flux measurements. Simulation results showed that carbon absorption and fixation increased during spring and summer because of enhanced photosynthetic activity, whereas carbon storage remained relatively stable throughout the year. Residual ponding during ebb tide significantly influenced DIC and TA concentrations via benthic mineralization and calcium carbonate (CaCO₃) dissolution. Comparative analysis revealed that the presence of mangroves increased carbon absorption, fixation, and storage by factors of 9, 3, and 6, respectively. These findings demonstrate that high-temporal resolution ecosystem models can effectively reproduce key material cycling functions of mangrove ecosystems and contribute to more accurate assessments of Blue Carbon dynamics in intertidal wetlands. EMAGIN-B.C_MG provides a novel framework for evaluating the carbon mitigation potential of mangroves in the context of climate change.