Abstract: When ships pass through a lock in the canal that connects the rivers and sea, the salt in seawater would invade into the freshwater area by the density current to affect the regional water quality of freshwater area and the living environment of freshwater aquatics. To analyze the saline exchange and transport characteristic during ship lock operation process, taking the proposed ship lock in Nicaragua Canal as the research object, we set up a coupling saline exchange model and three-dimension numerical model to simulate the step by step intrusion process of sea water into all step locks chambers and the further transportation into the upstream fresh water area. The simulation results show that salinity changes periodically in all step locks chambers and upstream waterway and reaches to a dynamic balance after a period of ship lock operation. The upstream saline transportation can be divided into density current section, transition section and diffusion section. Saline intrusion quantity in one cycle reduces gradually and trends to be steady with the operation time increasing. Based on the simulation results of coupling mathematical model, a differential equation is set up to predict the average salinity in Nicaragua Lake. The computing results show that the salinity of lake water in future is far less than salinity bearing capacity of environment.