The fact of the matter is there are some rules that, while clear, are really hard to enforce without officials present.
In this case the guy told you he was taking a water break ... are you really going to tell him you are putting him on the clock for a water break after 2 long sets? It seems like you were having a nice match and putting your opponent on the clock for a water break would essentially end that.
In my mind you have two choices ... toughen up mentally and not let your opponents water break be an excuse for a loss or resort to similar unenforceable illegal tactics to send him a message.
"You should be playing linebacker, not singles."