To evaluate the effects of the Lake Transport (LKT) and Streamflow Transport (SFT) packages, we can run the model again without including those two packages. Deactivate those two packages in the Model|MODFLOW Packages and Programs dialog box. It will be necessary to run MODFLOW again so that options in the MT3D-Link package are specified correctly. After running MODFLOW and MT3D-USGS again, import the concentrations as before.
You can create a data set that shows the difference between the two models by subtracting the concentrations without the LKT and SFT packages from the concentrations in the model in which the LKT and SFT packages are used.
