It depends. The source code is available online from PSU. You can compile and enhance the code using visual studio platform. But you need to know which part you need to improve at first, the hydrodynamic part or water quality part?
What is the problem threaten the waterbody (the studied dam)? Which quality problem should you study and alleviate? Which processes should be considered, that CE-QUAL-W2 hasn't had the capabilities to simulate?
If you understand the problem accurately, the source code modification is not challenging. Many researchers around the world modified the model code.
The CE-QUAL-W2 source code is available in model webpage, and you can compile it in intel visual fortran as a component of visual studio.