I need to compare three indices that were measured at a few different sites, which means I can't use their actual values because they are inherently different (maybe use ranks...), and that they are paired because each site has values for each index. I want to compare them using two independent variables (in addition to their values, I am using the SD within each site as a second variable- but that's not relevant, I just wanted to explain myself better).

What would be the right test for these data?

Thank you very much,