Development of small islands requires an integrated approach to promoting sustainable development, namely balancing between economic use of natural resources and environmental protection. The precautionary approach and conservation are necessary to ensure that the use of space and natural resources available in it is capable of supporting human life and protecting the environment. In accordance with their characteristics, management of small islands and coastal waters needs to be done in an integrated approach by using management model of small islands cluster and surrounding coastal waters. One method that can be applied is with spatial planning that promotes management of small islands and coastal waters according to the characteristics and the uses of space, natural resources, land and waters. To be effective it needs commitment of all stakeholders, cooperation between governments at all levels, and public participation.