In situ measurement of water spectrum is the basis of the validation of the ocean color remote sensing. The traditional method to obtain the water spectrum is based on the shipboard measurement at limited stations, which is difficult to meet the requirement of validation of ocean color remote sensing in the highly dynamic coastal waters. To overcome this shortage, continuously observing systems of water spectrum have been developed in the world. However, so far, there are still few high-frequency observation systems of the water spectrum in coastal waters, especially in the highly turbid and high-dynamic waters. Here, we established a high-frequency water-spectrum observing system based on tower in the Hangzhou Bay. The system measures the water spectrum at a step of 3 minutes, which can fully match the satellite observation. In this paper, we primarily developed a data processing method for the tower-based high-frequency water spectrum data, to realize automatic judgment of clear sky, sun glint, platform shadow, and weak illumination, etc., and verified the processing results. The results show that the normalized water-leaving radiance spectra obtained through tower observation have relatively high consistency with the shipboard measurement results, with correlation coefficient of more than 0.99, and average relative error of 9.96%. In addition, the long-term observation capability of the tower-based high-frequency water-spectrum observing system was evaluated, and the results show that although the system has run for one year, the normalized water-leaving radiance obtained by this system have good consistency with the synchronously measurement by Portable spectrometer ASD in respect of spectral shape and value, with correlation coefficient of more than 0.90 and average relative error of 6.48%. Moreover, the water spectra from high-frequency observation by the system can be used to effectively monitor the rapid dynamic variation in concentration of suspended materials with tide. The tower-based high-frequency water-spectrum observing system provided rich in situ spectral data for the validation of ocean color remote sensing in turbid waters, especially for validation of the high temporal-resolution geostationary satellite ocean color remote sensing.