The Java Sea with a surface area about 467.000 km2, is located in the South East Sunda Shelf with the average of depth is 40 meters, affected by several phenomena, whether physical or meteorological. This research aims to analyze the characteristics of water masses in the Java Sea and its relationship with the periodicity of the monsoon and Indonesian Throughflow Water (ITF) phenomenon. Then analyze the exchange of water masses in the Java Sea. The data used are temperature and salinity to identify the characteristics of the water masses. Ocean currents data to identify ITF patterns and winds data to identify the monsoon patterns. The data used in 2015 from the Infrastructure Development of Space Oceanography (INDESO) sites with a resolution of 1/12°. The method used is a descriptive analysis of spatially and temporally. The results show that averaging seasonal found that southeast monsoon period salinity is higher (31-34 psu) than northwest monsoon period (29.5-33 psu), and southeast monsoon period temperature is lower (27-30.5°C) than northwest monsoon period (28.5-30.5°C). ITF phenomenon occurs in May through September and reaches its peak in June, July, and August. ITF strengthened in southeast monsoon and weakened in the northwest monsoon. ITF and monsoon have similar impacts on salinity and temperature in the Java Sea. The water masses in the Java Sea comes from the South China Sea and Makassar Strait. In the northwest monsoon, Java Sea filled by water masses of the South China Sea, while in the southeast monsoon phenomenon which coincides with ITF phenomenon, Java Sea water masses is filled by water masses from Makassar Strait. In the transition monsoon I and II, the Java Sea filled by the South China Sea and the Makassar Strait water masses.