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A vertical (laterally integrated) two-dimensional numerical model was applied to study the salt water intrusion in the Tanshui River estuarine system, Taiwan. The river system has experienced dramatic changes in the past half century because of human intervention. The construction of two reservoirs and water diversion in the upper reaches of the river system significantly reduces the freshwater inflow. The land subsidence within the Taipei basin and the enlargement of the river constriction at Kuan-Du have lowered the river bed. Both changes have contributed farther to the intrusion of tidal flow and salt water in the upstream direction. The model was reverified with the earliest available hydrographic data measured in 1977. The overall performance of the model is in reasonable agreement with the field data. The model was then used to investigate the change in salt water intrusion as a result of reservoir construction and bathymetric changes in the river system. The model simulation study reveals that significant salinity increases have resulted from the combined changes. It has been speculated by ecological researchers that the long-term increase in salinity might be the driving force altering the aquatic ecosystem structure in the lower reach of the estuary and the Kuan-Du mangrove swamp, particularly the enlargement of the mangrove area and the disappearance of freshwater marshes. However, concrete proof has not been available since no prototype salinity data were available prior to the reservoir construction. This case study offers the first quantitative estimate of the salinity changes due to human interference in this natural system. [ABSTRACT FROM AUTHOR]