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Probably a geeky question, but how is it that my tank has high ammonia and low pH? Given that pH is=Log[NH4]. That would seem to indicate that if ammonia was high then the pH would have to be high. Are we talking about the difference between NH3 and NH4 (ammonia and ammonium) or what? Let me here from a Chemistry major

I am not a chemistry major (marine biology) but maybe I can help some. Ammonia NH3 is a weak base while Ammonium NH4+ is a weak acid. Acidic pH is low so if your ammonium(NH4+) is high it would make sense for the pH low. You might want to check and see what which ion kit actually test for(mine doesn't specify). If it does test for Ammonia NH3 it might have something to with the other ions in your water. As pH=-log[H+] and there may be other things in the water removing H+ ions or adding OH- (basic) ions. I believe nitrate/nitrite are also acid base pairs so it you might want to test those levels. My tank had the same problem. I hope I helped some. If not I will ask my roomate she is a chem major.