Hyperspectral sensor can confirm more exact material property because spectrum bandwidth is more details than multispectral sensor. Actually, it is not many reported previously, measurement of climate change, vegetation and ecology environment using hyperspectral sensor based on satellite, airborne and fixed ground are used in the world. However, water quality management using hyperspectral imaging system is limited and temporary. Therefore it is not enough data library to apply management of water environment with hyperspectral sensor. In this study, water quality analysis methods using hyperspectral sensor based on principle of NIR, FTIR and Raman spectroscopy to apply analysis organic compounds in water were described. This study will provide good information for many applications to control water quality of river and treatment water.