Lagoon Jusan is located in Northern part of the Japan main island. The lagoon is famous countrywide for catches of a bivalve, Corbicula japonica, and for its taste. However, the catches of the bivalve have been decreasing in recent years. One of the possible factors is influence from changing aquatic environment in and around the lagoon. In this study, continuous monitoring of salinity, dissolved oxygen and chlorophylla using auto-recording device was conducted during a summer season, when growth and spawning of the bivalve are the most active. The results of the monitoring and other measurements show that the water in the lagoon is generally rich in nutrients, organic matter and growth of phytoplankton, and that dissolved oxygen concentration sometimes declines. Numerical simulations were also conducted to understand spatial and temporal structure of water quality. The model applied in this study had a vertical 1-dimensional assumption. The results revealed that the stagnant water body tends to develop in the middle layer of the lagoon, even though the lagoon is quite shallow. This phenomenon promotes growth of phytoplankton.