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Mitigating climate change and managing land sustainably depends on understanding and quantifying carbon dynamics in ecosystems. Here we present a framework to integrate advanced direct carbon flux measurement techniques (e.g., eddy covariance and chamber methods) with spatially explicit ecosystem service modeling through the invest (Integrated Valuation of Ecosystem Services and Tradeoffs) framework, which can be applied across a diversity of ecosystems (e.g., coastal wetlands, mangroves, seagrass, forests, grasslands) to increase the spatial and temporal precision and meaningfulness of ecosystem carbon accounting and valuation.The methodology presented makes use of high-resolution land use and land cover (LULC) data and field-measured carbon pool parameters (i.e., aboveground biomass, belowground biomass, soil organic carbon, litter pools), as well as direct flux data from eddy covariance systems, in two ways: as direct empirical inputs quantifying net ecosystem exchange (NEE) that are site- and time-specific rates of carbon accumulation or emission, and as necessary standards for comprehensive model calibration and validation. The twofold utility of direct flux data reduces errors associated with prevalent generalized carbon stock assumptions and allows full representation of variability in carbon flux under different land-management and disturbance regimes.We apply this integrated framework to simulate carbon stock dynamics and annual carbon sequestration rates under various land-use change and ecological restoration scenarios. The spatially explicit outputs include detailed ecosystem maps of carbon storage, flux rates, and net carbon budgets that can inform targeted conservation and sustainable use strategies. Merging these adaptations to biophysical outputs with economic valuation problems that incorporate current pricing schemes in carbon markets and the social cost of carbon will allow stakeholders and policy makers to efficiently evaluate trade-offs among ecosystem services, economic returns, and climate benefits.Our approach is scalable and adaptable, allowing decision-making to occur over a range of biological contexts from dynamic coastal ecosystems that are subject to anthropogenic disturbance to more stable terrestrial biomes. This combination of research will allow for climate change initiatives to be implemented with vigorous due assessment of data-driven evaluation tools that will further the advancement of the dual goals of carbon neutrality and resilience of existing ecosystems to degrading events. These systems allow for direct measurements of relevant fluxes within complex models that engage ecosystem services and make them viable, filling important gaps in the understanding of empirical data relevant to ecology, biogeochemical modeling, and realistically set policy guidelines.Keywords: Carbon Flux, Coastal Ecosystem, Eddy Covariance, Ecosystem Service Modeling, Climate Mitigation, Carbon Market Valuation.