I don't have a suggestion that's specific to Croatia, but in general, I would prefer to find somewhere I can lock my valuables, whether that's a hotel safe or a storage locker somewhere.
Sometimes you have to pick the least bad option. Would you feel more secure leaving your passport tucked into a corner of your luggage in your B&B or in the trunk of your rental car, or under a towel on the beach? Or would all of these options be beyond your comfort level, in which case you could take turns going into the water while one person stays behind and keeps an eye on your valuables, or not go in the water at all, or go wading while you carry your valuables above water level.
I'll be curious to read what other travelers prefer to do.