There are several ways of controlling the output generated by MODFLOW.  The Output Control Option allows the user to specify when when heads, drawdown, water budget, and IBOUND are printed in the listing file or saved to an external file.  If the Output Control Option is not used,  head and overall budget are written to the listing file (printed) at the end of every stress period.

For transient models, the size of the output files generated by using the Output Control Option can become very large.  If the user is only interested in the a record of head or other variables at a few selected locations, the HYDMOD Package can be useful.  In it, the user specifies the locations of interest and the selected data for that location is written to a file at the end of every time step.  Such files are generally compact.  A similar capability is provided for the Lake and Streamflow Routing (SFR) packages by the Gage package.

If the user wishes to use the solute transport model MT3DMS, one of its input requirements is a file specifying the fluxes between cells for each stress period.  This file can be generated by using the Link-MT3DMS Package and then used as an input file for MT3DMS.

The following packages have their own built-in forms of output control.