I have some suggestions:
- Do a sequential calibration, first calibrate your flow (which you already did), then fix the flow parameters, and then only calibrate the nitrate load. Doing this secures that you are only modifying nitrate process.
- Add more nitrate related parameters. Check how SWAT modelates the nitrate load in the 2009 Theorical Manual. It gives you an idea on how it works.
- Do not expect good results for nitrate, as far as I now, it is really hard to calibrate some variables in SWAT. If you are calibrating on monthly time step, then you have more chances to get decent results. If you are doing it daily, then your chances decreases.
Regards,
Oscar