Recently, Andong Reservoir and Imha Reservoir located in Nakdong River basin (Korea) are being connected by a tunnel (length 2km, diameter 5.5m) for a conjunctive use. The objectives of this study were to construct a two dimensional(2D) laterally-averaged model for two reservoirs, and examine the effects of connection on the water transportation and temperature stratification in the reservoirs. The 2D models for each reservoir were calibrated using field data obtained in 2006, and applied to the linked system for the year of 2002 when a severe flood intruded into Imha Reservoir during the typhoon Rusa. Simulation results showed that 364 million $m^3$ of water can be conveyed from Imha to Andong, while 291 million $m^3$ of water from Andong to Imha after connection. It resulted in 1.38 m increase of annual averaged water level in Andong Reservoir, whereas 3.75 m decrease in Imha Reservoir. The structures of thermal stratification in both reservoirs were influenced in line with the flow exchanges. In Andong Reservoir, the location of thermocline moved upward about 10 m compared to an independent operation. The results imply that the persistent turbidity issue of Imha Reservoir might be shifted to Andong Reservoir during a severe flood event after connection.