I don't think it's likely that he's has the flush. He probably called the flop bet with an overpair or a 10 (like an A10. Maybe the club flush draw. The turn is a blank so he thinks he's still good.
This is $2nl so people will stack off with top pair (sometimes less ) and also draw way against the odds
. I think you're way ahead or someone just sucked out bad on you, which is cool, it happens. You want them drawing against the odds. That's money in your account over the long term.
Personally though, I think you're way ahead. The real question becomes how do you get the most value out of the hand. If you're gut says he'll bet the river thinking he's ahead, check/call. If you think he's a station, bet fairly big. Or, if you're worried, you could throw out a smallish blocker bet to get looked up by two-pair type hands and fold to a raise. I vote is to bet for value though. It's about feel at this point by how you want to do that.