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Abstract The strength of coastal Arctic Ocean CO₂uptake is vulnerable to landscape‐scale changes such as hydrological intensification, changing climate, and alterations to terrestrial and aquatic biogeochemistry. Across a period of 4 yr (2019–2023) and three distinct sampling periods, we visited five coastal ecosystems of the Beaufort Sea with varying barrier island coverage to understand drivers of Arctic coastal CO₂flux. The ice cover sampling period was characterized by the highest pCO₂saturation and dissolved O₂undersaturation. We observed a > 100μatm difference in pCO₂over shallow depths (up to 2 m) at 73% of ice‐cover site visits. Notably, the geomorphology of barrier islands and channels controlled the flushing of colder Beaufort Sea waters across the systems and influenced the strength and appearance of both vertical thermohaline and pCO₂stratification. The ice breakup period reflected spring freshet and was a net CO₂sink during sampling, likely related to freshwater riverine dilution, CaCO₃dissolution from sea ice melt, and water column algal activity. During the open water sampling period, the interaction of marine and terrestrial contributions predicted the strength of the CO₂efflux, with freshwater inputs introducing higher temperatures and organic material, which increased remineralization. The capacity of these systems to act as CO₂sources or sinks varies throughout the year and is largely driven by geomorphic conditions. Any spatially integrative studies of CO₂flux or coastal productivity should consider the physical and biogeochemical heterogeneity of Arctic coastal ecosystems.