A water quality model, including salinity and temperature, has been linked to a one-dimensional, MIKE 11 hydraulic model of the northern part of the Sacramento-San Joaquin Delta (the North Delta). It was produced to examine any water quality effects that the restoration might have on the region, the effect of regional scale changes on the restoration area and to produce local boundary conditions for future multi-dimensional modeling of the restoration area. Temperature and electrical conductivity data were collected at the boundaries of the North Delta model to facilitate the calibration and verification of the water quality model. Continuous water quality data was collected in order to create a database used in this study and possibly in future studies in the North Delta. The model was used to examine various restoration alternatives involving McCormack-Williamson Tract and the Delta Cross channel during the summer low flow periods. The results from the model illustrate that the restoration alternatives which change flow also alter the water quality. It was discovered that the restoration alternatives involving McCormack-Williamson Tract produce highly localized changes in water temperature and electrical conductivity around the altered tract while only slight changes occur upstream and downstream. Furthermore we found that the MIKE 11 water temperature model can only capture general trends, neglecting smaller events that can occur.