Hi Qais,
To do Climate Change projections using SWAT:
1ST, you must select the appropriate future range of year based on your historical data: If you have 30 years of history and must compare it to 30years in the future. Because it doesn't make sense to compare 30 years of historical data with 5 years of the future (you see my point)
2nd You must use different projections (GCMs' outputs) for every scenario (RCPs or SSPs for the CMIP5 and CMIP6 respectively) that you are working on, because nobody can predict the future, so when we are talking about projections a range of variation is more useful than give a single value.
3rd Do not forget that the results that SWAT will give you are approximations, sometimes we overlook the fact that SWAT has a lot of simplifications in how it models our study area.
Kind regards,
Oscar M Cabezas-Nivin