Strange, I have sinus issues also and I am on Plaquenil but I think with yellow and green discharge you absolutely need to see your doctor. They can CT your sinuses and do sputum tests to see if anything comes up. Even test for the flu. I really CANNOT say this is related to the medication as I have GERD and other issues but the congestion started with my auto-immune issue. For 5 years I\'ve been spitting up phelm, mostly in the a.m. when I wake up as I think it is in my sinuses and lands in the throat while I lay down. I\'ve had numerous tests and so far no luck diagnosing. Could be allergies as my immune system is not up to par. Good luck.