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The coral reef ecosystems around the world are under the influence of both natural and human factors, which lead to critical ecosystem degradation and unrecoverable effects. To understand the influence of environmental factors on coral reef ecosystems, this study adopts the idea of taking the whole ecosystem as an integrated one. By applying the Multiple Systems Coupling (MSC) method, an interference mechanism model is built in this research to combine the internal biotic community factors in the coral reef ecosystem and the external environmental factors in order to generate an integrated spatial model of the coral reef ecosystem. The model built in this study is tested on the Boa-Li watershed in the south of Taiwan. The research investigates how increased runoff pollution due to the change of basin land use and land cover structure contributes to the phenomena of benthic community changes. The results of this study showed that comprehensive management of the Boa-Li estuary basin can stabilize flow to reduce the level of water pollution, contributing to the recovery of the coral reef benthic community. The comprehensive management plan should be able to reduce the influence from the possible increase of land-based source pollution on the coastal coral reef benthic community, which increase is brought by the Boa-Li estuary basin Strategic Plan for National Spatial Development. Therefore, the creation of the coral reef ecosystem system model can contribute to the understanding of environmental influencing factors and their damaging effects on the coral reef ecosystem. This study can also serve as a reference for policy-making regarding coral reef ecosystem conservation.
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