The Indonesian waters, located in the tropical area between the Pacific and Indian Oceans, comprise shelf and deep sea areas with their special characteristics. The Java Sea, as one of the shallow waters areas in Indonesia, has an average depth of about 40m, low salinity and high temperature. South of Java is the deep eastern Indian Ocean which is characterized by high salinity and low temperature. Both water masses are interacting and mixing through the Sunda Strait. Although the Sunda Strait is a small passage, its role in influencing the ocean climate variability is quite important and will be discussed as the main topic in this study. The HAMburg Shelf Ocean Model (HAMSOM) is used to simulate the long period ocean-climate dynamics in the Java Sea and the eastern Indian Ocean. Numerous simulations and boundary treatments are performed to get results that best agree with the observations. Forcing data from 44 years (1959-2002) NCEP reanalysis are used in the simulation to analyze the variability of current circulation, water mass transport, upwelling south of Java, and the effect of ENSO (in the Pacific Ocean) and DME (in the Indian Ocean) to this area, as well as their interaction.