Estuarine zone is a typical ecosystem, because this areacontinuously receives organic materials from the river and sufficient light illuminating the water. It has also salinity level from mesohaline to eurihaline. The zone must be protected from waste discharge (liquid or solid) coming from domestic and industrial activities along the riverside. The determination of estuarine boundary still cannot be confirmed until now due to the transformation of existing water dynamics changes over time according to the season changes. One of technologies in the determination of estuarine boundary is using remote sensing technology.The advantage of this technology is on its temporal and spatial resolution. Some research have been done in tropical water of Northern Java Coast and Makassar Strait, however none has been done in tropical high seas such as in Cimandiri Estuary. The algorithm model resulted from this research is different with existing algorithm. Estuarine boundary will be made based on salinity level. This model can also be used for different area and used by stakeholder and local government in order to protect estuary in sustainable way.