This study aims to examine the characteristics of the water quality variation in relation to the change of water exchange rate with respect to the development phases of the Pusan port. To clarify the characteristics, water exchange caused by the variations of coastline shape and water surface area was examined by the numerical experiments using the Lagrangian particle tracking model based on 2-D shallow water equation. As the results of numerical experiments, it was proved that the water exchange in the Pusan port was decreased mainly due to the port development and the breakwaters construction. During the port development phases from 1875 to 1998, 35% of the sea-space in the port had decreased to make hinterland spaces. This resulted in the loss of wet-land and coastline change as well as decrease of the water exchange rate at the sea side. The city population in that period had rapidly increased from several thousands to 4 millions, resulting in the large discharge of sewages into the port area. Under the these environmental conditions, it can be clearly said that the water quality in the Pusan port is sensitively affected by the discharge of urban sewages decrease of the water exchange rate in relation to port and urban developments. In the study, the temporal changes of water quality were discussed with respect to the port development phases. It was clear that the water quality wad controlled by the exchange rate change under the port development as well as the input impact into the port from the urbanized city area. To make clean sea of the Pusan port, it is suggested that the sewage control, the water exchange and coastline control should be systematically checked under the concept of eco-friendly development and environmental management.