Monitoring programs provide ongoing information on the state of the marine resources that can be used for adaptive management, to assist in prioritizing monitoring and research activities, and to inform management decisions. Populations of key conservation species were monitored to assess the success of MPAs, e.g. coral reef fish larvae have been monitored to determine the connectivity among protected areas of the MAR. Also, the baseline for mangrove and sea grass cover was established in the four protected areas. The resulting datasets and subsequent analyses provide essential information to inform adaptive management strategies and assess the management effectiveness of the marine protected area. The monitoring programs also included capacity building activities for staff, rangers and community members to conduct research and monitoring as well as to improve support for conservation activities.

To ensure that the conservation values of the protected area are effectively protected, interested community members are trained in monitoring of trends in fish and invertebrate populations using standardized techniques. Selection of trainees and implementation of continuous monitoring are done in coordination with the community’s management committee.

In order to ensure that the scenery values of the area are effectively protected, interested community members are trained in monitoring of scenery values using standardized techniques. Selection of trainees and implementation of continuous monitoring are done in coordination with the community.

A monitoring system is used to measure sediment accretion, and to monitor the condition of the T-fences. In addition, natural regeneration of mangroves is monitored. During the first year after construction, functionality of the T-fences should be ensured through monthly visual inspections and maintenance where necessary. After one year, visual inspections and maintenance should be carried out at least after the end of every storm season. In addition, seasonal GPS surveys of the shore line at low tide can be used to see whether the T-fences have impacts on the shape of the coastline nearby. The natural regeneration of mangroves is documented by recording species, size and density or through fixed-point photos. The latter can also be used as a simple alternative for GPS shore line surveys.

A pluralistic governance board is typically composed of representatives from local authorities, government departments and agencies, local communities and sometimes business organisations and is established during a negotiation process. The board is responsible for making joint decisions about issues raised regarding natural resource conservation. Its role is steering the implementation of the co-management agreement and review of the co-management results and impacts based on monitoring. The pluralistic governance board is an essential element to turn the idea of "sharing power" from theory into practice. This distinguishes it from centralized or private management where only one partner assumes the responsibility for making decisions.

The co-management agreement is a document consisting of everything agreed to during the negotiation process including management and governance elements. It can be seen as written evidence of the partnership among local actors. The management part specifies the six ‘W’: who can do what, where, when, how and how much. It provides general conditions; specifies natural resource management rules and regulations in each zone, rewards, penalties, the reporting schedule and implementation terms and monitoring. The governance part specifies key actors for decision making and their responsibilities.

Local institutions and communities, municipal and national govern¬ment representatives, NGOs, academia, and the private sector are all represented in a locally-based park management and law enforcement body. Law enforcement is ensured through partnerships with the Philippine Navy and Coast Guard and locally recruited park rangers who receive in-depth training and appropriate surveillance equipment. The environmental situation in the park is monitored regularly, while the effectiveness of governance is measured annually using participatory mechanisms.