I'm not sure how to solve your problem exactly, but I'm going to respond here assuming you were attempting to implement an atmospheric boundary condition at the top of a water column or unsaturated zone...
If you made a boundary element for the atmosphere with very large volume, you can change the pressure in that volume over time with a source (or sink) with suitable injection (or production) rates. See Section 7.2 of the TOUGH 2 User's Guide, starting on page 62. Once you have that pressure vs. time set up properly in that element, the evaporation occurring in the elements beneath it should take care of itself.
I hope this helps get you started! If this doesn't describe your problem sufficiently, please send me more details about what you're trying to do.