The Raja Ampat MPA Network Technical Management Authority (UPTD) conducts biological monitoring of the reef ecosystems including monitoring of benthic communities (particularly corals) and populations of important fish that are indicator species. These results are used to assess the health of the reef and assess the effectiveness of MPA management in protecting biodiversity and maintaining or increasing the abundance, size and biomass of reef fish. This monitoring is done repeatedly to observe changes in condition and evaluate progress towards achieving the management objectives of the Raja Ampat MPA network.

The UPTD also monitores the utilization of marine resources. These monitoring activities provide information and data on how fishermen in Raja Ampat utilize its resources (what tools are used for fishing, when, where, and by whom). Information on the types of marine resource use is crucial in adapting and improving the planning and management of the Raja Ampat MPA network.