<p>Mangroves are at the frontlines of climate change impacts and rapid urbanization, resulting in an urgent need to protect their structural integrity and long-term sustainability. Traditional monitoring approaches ignore the hidden degradation of mangroves caused by fragmentation and human activities. We developed a dual-index framework to assess mangrove resilience and sustainability trend in Balikpapan Bay, which is under increasing pressure from the rapid urbanization due to Indonesia’s new capital development. The framework uses principal component analysis to integrate eight sub-indicators of mangrove structure and function, analyzing spatial transitions at 5-year intervals from 2010 to 2020. Results show that the total mangrove area changed by less than 0.7%, but in low-sustainability trend cluster high-resilience mangrove zone declined by 65% and medium-resilience zone expanded by 159%. Although dynamics centered on key transition zone involved over 110,000 pixels shifts, the actual area just achieved a net growth of 1.5%, indicating recovery limitations in mangrove area. Our findings identify productivity and human disturbance as primary drivers that jointly control mangrove functional sustainability trend and structural resilience. These insights contribute to reducing human disturbance impacts and enhancing productivity to sustain ecological functions, and provide a universal tool for mangrove management in coastal regions facing rapid urbanization.</p> Graphical Abstract <p></p>