In this paper, we study salinity transport in a section of the Mekong Delta river system in the Tra Vinh district of Vietnam. A combined linear state space model is developed for the shallow water flow and salinity transport in the presence of a sluice gate crossing the river. A Linear Quadratic Regulator (LQR) optimal control method is used to derive the gate closure rate that can minimize salinity intrusion from the sea and associated costs due to loss of farming and transportation revenue. Results are verified via simulations.