Groudon with 0 SpD IVs, -SpD nature:
252 SpA Rayquaza Waterfall vs. 0 HP / 0- SpD Groudon: 277-326 (81.2 - 95.6%) -- guaranteed 2HKO
Groudon with 0 SpD IVs, neutral nature:
252 SpA Rayquaza Waterfall vs. 0 HP / 0 SpD Groudon: 248-292 (72.7 - 85.6%) -- guaranteed 2HKO
I'm assuming you're in Gen 3, since you gave your SpA EVs. If Rayquaza didn't have Air Lock, Drought would weaken Waterfall enough to safely use it. But since Air Lock negates that, you do run the risk of getting either a high damage roll against the absolute lowest SpD Groudon can have (unlikely) or critting (much more likely, at 6.25%), both of which will be enough to KO after the Ancient Power you already used. Both are pretty unlikely, but if for some reason you cannot afford to lose this Groudon (like if you forgot to tell us that it's a shiny or something), then be aware that there is a risk.
Assuming, of course, that you kept you haven't continued the battle in the 10 hours it took for you to get an answer, which I suppose is rather unlikely.