Urban coastal ecosystems, which are strongly influenced by human activities and elevated nutrient inputs, can contribute to climate-change mitigation through carbon uptake, fixation, and storage. However, it remains unclear how the underlying carbon-control structures governing these functions respond to nutrient enrichment, owing to the interactions of multiple biogeochemical processes across pelagic and benthic systems. In this study, we applied the benthic–pelagic coupled ecosystem model EMAGIN-B.C. ver. 2 to Tokyo Bay to examine how nutrient loading influences carbon cycling in urban coastal environments. To interpret these responses mechanistically, carbon cycling was organised into three paired flux balances representing carbon uptake (A/R), carbon fixation (F/U), and carbon storage (S/D). These functional pairs were analysed within a conceptual framework of a Dual Carbon Loop consisting of organic and carbonate pathways. Model simulations demonstrate that increased nutrient loading enhances atmospheric CO₂ uptake and pelagic carbon fixation. However, the dominant mechanisms controlling carbon cycling differ substantially across regions. In the estuarine region, nutrient enrichment amplified pelagic primary production, resulting in simultaneous increases in carbon uptake, fixation, and organic carbon burial. In the central bay, production and remineralization are intensified in tandem, indicating strong internal coupling of carbon fluxes. In contrast, tidal flats exhibited a transformation-dominated response wherein externally supplied organic matter was rapidly processed by benthic communities, thereby limiting net pelagic fixation while maintaining relatively stable carbonate storage and producing a system characterised more by transport, transformation, and redistribution than by new production. These contrasting responses indicate that identical nutrient forcing can produce distinct carbon-cycling behaviours depending on the regional ecosystem structure. We interpret these patterns as spatial differentiation of carbon-control structures governed by the relative balance of opposing carbon fluxes within the Dual Carbon Loop system. The proposed framework provides a mechanistic basis for understanding how nutrient management influences climate-mitigation functions in urban coastal ecosystems and offers a perspective for analysing shallow, nutrient-enriched coastal systems characterised by strong benthic–pelagic biogeochemical coupling.