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Rarotonga the capital of the Cook Islands is rapidly developing with tourism as one of the major income earners for the country. The health of the lagoon and reef is important for the welfare of the people. It is vital that the health of the lagoon is monitored and action is taken to protect the health of the lagoon, coral reef and the people that use it. Human activities contribute to the decreased water quality, for example farming of pigs, deforestation and farming crops close to streams. The water quality monitoring programme gives an evaluation of the state of the streams and lagoon, and can be used to identify issues that need to be addressed.

Coral Reefs and their associated habitats are recognised as an extremely important resource throughout the South Pacific region. Fiji is one of the wealthiest countries in the region. This is in part attributable to its biodiverse and productive reef ecosystems, which provide valuable fishery resources, important tourism attractions, as well as protection from storms and coastal erosion. Over recent decades, there has been a glowing realisation of the degradation caused to coral reef environments due to increased coastal development and resource over-utilisation (Hodgeson. 1999). These threats may manifest themselves as increased nutrient enrichment, erosion, siltation. over fishing, destructive fishing, marine pollution, and well as harvest for the aquarium trade. Such impacts, often acting synergistically with natural impacts, can result in a decline in ecosystem productivity and stability. Left unchecked this will ultimately lead to a reduction in income and resources for coastal communities and other stakeholders that rely on fishing and the marine environment.

Fiji is one of the wealthiest countries in the South Pacific, partly because of its extensive marine resources, which provide important services such as protein from fishing and income from tourism. The country is made up of approximately 844 volcanic islands and is dominated by the Viti Levu and Vanua Levu platforms which account for 87% of the total land area (Vuki et al., 2000). Fiji has a moderate tropical climate and hence reefs are well developed around all of the islands.