Hi,
I have read quite a few posts about SWAT under Linux and I think you can try my method if any of you still have issue.
I recently tried to compile SWAT from source code using makefile and CMake, it worked after fixing some errors.
The step-by-step instruction is hosted on Github now.
You can use the modified source code from the repository or you can edit the source code (version 664 at the time of testing) following my comments on Github.
After the CMake build, you will have the following tree structure:


If you prefer to use ifort other than gfortran, leave a comment, I may add that later.
Good luck!
--Chang