I don't think you can ever be 100% sure the policy will not have changed the week before your arrival, so I wouldn't take an expensive water bottle to any indoor sight. I take a couple of disposable ones with me on each trip and use those when I'm sightseeing. This time I also threw a reusable bottle in my suitcase, and I've used it almost exclusively in my hotel rooms.
On the other hand, virtually all indoor museums have lockers where you can stash belongings. The only potential issue is locating an empty one at busy times; you might have to hang around for a few minutes until someone empties a locker. Fancier lockers are sometimes broken, I find, which doesn't help with availability.
If the place isn't doing careful bag checks, you'll likely get by if you stuff the water bottle into a purse, assuming the purse isn't too large to be admitted. The Borghese in Rome either bans all bags or enforces a very small size limit, just as one example.