This research evaluates and improves capabilities incorporated in the Water Rights Analysis Package (WRAP) modeling system for tracking salt loads, particularly for applications dealing with natural salt pollution problems that are prevalent in several major river basins in Texas and neighboring states. WRAP is the river/reservoir system simulation model incorporated in the Water Availability Modeling (WAM) System applied by agencies and consulting firms in Texas in planning and water right regulatory activities. A salinity simulation component of WRAP called WRAP-SALT was developed recently at Texas A&M University. WRAP-SALT was based on the premise of complete mixing within the monthly computational time step. However, salt concentrations actually have time variation throughout a reservoir. This thesis research investigates more realistic salinity routing methods. Historical gauged data provide a basis for calibration of routing parameters. The timing of the inflow load to determine outflow concentration is calculated by lag parameters with the monthly time steps. Complete mixing occurs during the lag months. Two options are incorporated into WRAP-SALT for setting the lag parameter. With the first option, the model-user sets a constant that is applied during every month of the simulation. This option requires calibration studies to determine the lag. With the alternative option, a variable lag is computed within the model in each month based on the concept of retention time, which is a representation of the time required for a monthly volume of water and its salt load to flow through a reservoir. When the lag is activated, the accuracy between observed and computed mean monthly salinity concentrations through the reservoir is generally improved. The basin-wide simulation was performed for the Brazos River Basin for conditions with and without salt control dams proposed by the Corps of Engineers. The proposed salt control impoundments improve water quality throughout the basin.