<p>Urban areas in coastal regions are increasingly vulnerable to climate change but can serve as a pivotal starting point for climate mitigation. Understanding carbon dynamics in coastal urban areas is essential for sustainable development. This study investigates the influence of urban spatial structure (USS) elements on carbon emissions and storage in the Samarinda Metropolitan Area during 2021, prior to Indonesia’s capital relocation. Using Ordinary Least Squares and Geographically Weighted Regression, the study examines the impacts of USS elements (functional mix, built-up environment, and natural environment) on carbon dynamics across three different models (combined, coastline, and no coastline), emphasizing the spatial heterogeneity of these interactions. The findings reveal a higher concentration of carbon emissions on the eastern coast, while carbon storage across the region remained favorable due to the presence of extensive natural land covers. In the combined model, the cumulative impact of USS elements on carbon emissions was found to be stronger than their effect on carbon storage. Notably, USS elements’ influence on carbon emissions was more pronounced in inland areas (no coastline model), whereas their impact on carbon storage was stronger along the coast (coastline model). These results also underscore the spatial heterogeneity of the impacts, serving as the foundation for zone classifications. Finally, integrating carbon dynamics into urban planning can lead to more sustainable development in coastal region. This study highlights the need for targeted strategies that focus on specific spatial zones and USS indicators to effectively reduce emissions and enhance carbon storage.</p>