Evaluation of future Sacramento-San Joaquin Delta scenarios requires hydrodynamic and salinity transport modeling to assess water quality affects to both the environment and water supply. This paper compares modeling results from a simplified, tidally-averaged one-dimensional model of the Delta (WAM) with results from the coarse grid San Francisco Bay-Delta Unstructured Tidal, Residual, Intertidal & Mudflat Model (UnTRIM), a 3D adjustable bed hydrodynamic model (MacWilliams and Gross, 2007). UnTRIM provides finer scale input parameters and additional dimensionality not available in WAM. Modeling scenarios include zero, one and three feet of sea level rise, unimpaired Delta inflows, historical Delta salinities with no exports, in-Delta exports (current conditions), upstream exports from a 2,000 cubic feet per second (cfs) capacity pipe, and upstream exports from a 7,500 cfs capacity pipe, for 6 total scenarios. When salinity results were compared to regulatory thresholds, WAM and UnTRIM were found to provide similar trends. WAM thus becomes a useful planning model, demonstrating computational speed advantages over a 3D model while providing relatively accurate results for water supply and regulatory compliance purposes. Large differences occur at Collinsville, where UnTRIM results show much higher salinity than WAM results. This may be due to the relatively nearby WAM model domain in San Pablo Bay, the lack of Three Mile Slough in WAM’s network, the tidal averaging of WAM results, and/or WAM’s lack of wind representation. Results also show differences in sea level rise scenarios between the two models. Higher sea levels tended to raise salinity less in UnTRIM than with WAM. WAM may over-estimate the effect of sea level rise on Delta salinity. Differences in absolute salinity values up to 60% were noted for some cases and locations, however minimal differences in the time above thresholds were found. Thus, the results of Fleenor and Bombardelli (2013) are confirmed with a 3D model.