Are you positive about this? I might be mistaken (and, as a matter of fact, my statement was introduced by "I think"), but I recall some runs where this happened (1 of the 2 fountains in the north 5X5 puzzle room was activated?) and we still got the underwater chests. Memory could be really playing tricks on me ....
However, I wasn't suggesting to activate fountains before solving puzzles.... when this happens, it's often because of poor communication and coordination .....