This article demonstrates why it is necessary to have the restoration of marine coastal ecosystem health as a new goal for integrated catchment management in the coastal area of Tolo Harbor. The present goal of integrated catchment management (ICM) in the Tolo Harbor is based on water quality objectives. The performance of the ICM plan, the Tolo Harbor Action Plan (THAP), was evaluated using marine coastal ecosystem health indicators including both stress and response indicators. Since the implementation of THAP in 1988, some significant reductions in pollution loading have been observed: reduction of 83% of biological oxygen demand load and 82% of total nitrogen between 1988 and 1999. There has also been an improvement in the health of Tolo Harbor's marine coastal ecosystem as evidenced by trends in physical, chemical, and biological indicators, although reverse fluctuations in some periods exist. However, such improvement can only be considered as the first sign of complete ecosystem health restoration, because ecosystem health covers not only physical, chemical, and biological aspects of an ecosystem, but also ecosystem service functions. The findings support the need to take the restoration and protection of marine coastal ecosystem health as a new goal rather than using water quality objectives. Steps necessary to further improve Tolo Harbor's marine coastal ecosystem health are also discussed.