The present writers' contributions for the development of a long-term observation system were briefly reviewed. The developed system consists of an acoustic observation system and a water bottom thermometry system using an optical fiber distributed sensor. The former measures acoustic reflection caused by the rapid change of acoustic impedance at the boundary of the halocline in water, and the latter detects movement of the lower part of the lake or river water by means of temperature change. The CT multi-sensor cable remodeled by XCTD probes for measurement of salinity and temperature has also been developed. Long-term observations using these equipments were successfully carried out in Lake Nakaumi, and River Gonokawa as well. The efficacy of applying this system for the observation of oxygen-poor water mass, especially in the case of its invasion to Lake Shinji via Ohasi River is proposed.