My engine is clunking.. Water in it?

[The Cleaner]

If you have water in the combustion chamber there is only one way it would get there (short of a blown head gasket) and thats via the intake. The odds of enough water getting that far and past the air filter is next to impossible in any normal rain or heavy storm. If by some chance water did get past the air filter, past the MAF without damaging it and then to the composition chamber it would be turned to steam immediately. And you would probably not even notice. If enough water got in the intake to do any more than turn to steam your engine would lock up.
Without a OBD code triggered, you do not have a major problem, and probably not water related.