Ajkwa Estuary, located in Mimika Regency, Central Papua Province, Indonesia, represents a dynamic and biodiverse ecosystem that plays a pivotal role in providing ecosystem services. However, like many estuarine systems globally, the intensification of its use has led to significant environmental challenges. The estuary is particularly susceptible to ecosystem alterations caused by accelerated sedimentation from undeposited tailings originating from mining operations. This study investigates the novel approach to sedimentation area management involving the construction and deployment of estuarine structures, including Geotube and Bamboo E-Groins, to confine sedimentation within designated zones. These interventions aim to manage the land formation, facilitate mangrove colonization, enhancing the estuary's capacity for water conservation and carbon sequestration as a climate change mitigation measure. Empirical findings demonstrate that the implementation of 2,700-meter-long Geotube structures and 2,800-meter-long bamboo E-Groins effectively increased sediment deposition to a depth of 0.74 meters, creating optimal conditions for mangrove establishment. Mangrove seedlings introduced to the newly formed sedimentary zones exhibited a survival rate of 99%. Carbon sequestration potential was quantified for the 500-hectare mangrove-assisted colonization area, with results indicating an atmospheric carbon dioxide sequestration capacity of 422,272.08 tons CO2 equivalent, corresponding to 115,374.88 tons of stored carbon. Projections for a 50,000-hectare expansion of mangrove colonization suggest a total carbon stock of 3,953,566.77 tons, equivalent to the sequestration of 14,470,054.36 tons CO2.