The particular monitoring methods employed within an MPA will depend on the scope of the monitoring programme, which in turn depends on the critical questions that need to be answered. The techniques used to monitor cetaceans within an MPA will be driven the size of the MPA, the species present, and available human resources and budget [4].

All methods of monitoring marine mammals have their strengths and limitations. Given the limited (or insufficient) resources of most MPAs, and the difficulty of monitoring large and often wide-ranging animals, cost-effective strategies that utilise local people and MPA users can form an important component.

Some of the more cost-effective methods, though less rigorous, include recording incidental sightings from MPA users and stranding data. This data, though providing some indication of the species found in an area, generally cannot be used for quantitative analyses such as measuring population size [4].

Data collection from tourism operators, as well as citizen science can provide robust data, depending on the species and cost. Citizen science and ecotourism data collection are increasingly used in monitoring, and MPA managers can encourage this. One example is the site Happy Whale, where citizens are encouraged to upload images of whale flukes (tails) to a database, they are identified by their unique markings, and they then can be tracked around the world [5].

Other, more specialised methods will depend on the species, the research goals, and the available resources. These include passive acoustic monitoring, which is particularly useful in monitoring highly-vocal species of cetacean. Observational monitoring from land, sea, or aircraft, and Photo ID may all form a part of the monitoring mix. Satellite tagging is now, especially given the large distances travelled by the larger whales, a widely recognised method of monitoring cetaceans [6].

MPA managers, however, will likely not have the human or budget resources to run all elements of ecological monitoring. Existing scientific institutions are usually brought in as partners to help to design and fund monitoring programmes, and indeed to help define the major issues in the planning phase [2].