To investigate the halocline behaviour and water quality in brackish lakes and estuaries, we have already developed a long-term observation system. The system consists of an acoustic observation system and it measures acoustic reflection caused by the rapid change of acoustic impedance at the boundary of the halocline in water. Long-term observations using the system were successfully carried out in Lake Nakaumi. Salinity, pH, dissolved oxygen, water temperature, and water flow rate and direction were also investigated by the other equipments. The results suggest that the halocline is easily moved and its behaviour is influenced by wind significantly. In addition, a simplified model of the halociine behaviour with the wind velocity and the distribution of salinity has been developed. Through the data presented in this paper, the importance of integrated studies of halocline bahaviour, and the usefulness of the long-term observation system.