This part seems wrong: "Then I apply the money I collected in the Water Budget Account as a credit on their statement."
You apply their Payment. The Statement Charge for water, then gets Paid. You don't also give them Credit; that would reverse that you first charged them.
Here's how to do this:
You set up a Single-sided Other Charge type item and link it to Water income or Water Liability, to meet your accounting requirements.
You list this for the Statement Charge. That is how you collect the funds.
You list that same item on the Items tab of the Payment. That's how you show you Reduced the funds prepaid to you.
There is nothing to Credit Back to the owners. You are confusing either Income-Expense, or Liability-Cleared Liability, with a process that would turn this into "Liability prepaid, actual owed, prepaid applied." Those are Three Different Concepts.
Which do you want to be doing?