Mangroves are important ecosystems that provide a huge range of benefits for coastal communities. The management of mangroves requires multiple methods and approaches that contribute to answering the policy relevant questions. Our site is in the Perancak estuary, Bali, where mangroves were degrading in 1980's due to the conversion of mangrove forests to aquaculture ponds and later reestablished in early 2000 when many aquaculture ponds were abandoned due to economic crisis and the diseases. Monitoring of mangroves in this area has been conducted since 2004, aiming to identify the ecological processes in mangrove ecosystems that support mangrove conservation initiatives and coastal management. The study showed the recovery in net primary productivity (NPP) and carbon sequestration capacity of mangroves in abandoned ponds. Our results support the view that mangroves are highly productive ecosystems that can recover from disturbances even from extensive land conversion through destruction of mangrove trees, and undertake reshaping of hydro-biogeochemical processes. Mangrove extent can grow by self-regeneration and replantation throughout the 7.5 km² estuary, this resulting in the reverse process of aquaculture site conversion into mangroves areas. In the frame of the INDESO project (Infrastructure Development for Space Oceanography) mangrove changes in this region are monitored in support of a series of very high resolution satellite images acquired since 2001. The analysis of these data supports the definition of keystone regions for monitoring biodiversity recovery and ecosystem protection. Our goal is to provide recommendations for sustainable management of mangrove coasts that are understandable to local government and stakeholders, including the recommendation that supports the establishment of Regional Marine Conservation Area (or Kawasan Konservasi Laut Daerah, KKLD) of the Perancak estuary.