Blue carbon ecosystems (BCEs) are well-recognized for their considerable potential in climate mitigation. However, current understanding of carbon (C) gains and losses of BCEs is rarely based on a net ecosystem carbon budget (NECB) framework, which incorporates all C budget components. We propose a comprehensive NECB framework for BCEs that includes C inputs from riverine flows, exchanges between the Earth's surface and the atmosphere, burial in sediments, and exchanges between BCEs and the continental shelf. Focusing on the Yellow River estuary in China as a case study, we applied the proposed NECB framework to quantify the C budget of this BCE. We show that C balance assessments of BCEs that rely solely on limited measurements of C accumulation rates or C flux are characterized by large degrees of uncertainty. The proposed NECB framework could improve our understanding of the role of BCEs in climate mitigation. We emphasize the need for revisiting the C balance of BCEs using an NECB framework, which integrates multi-disciplinary approaches.