Lake Naujan is so environmentally clean that there are parts of it in which the water can be safely drunk directly by humans.
However, this pure water finds its way to Puerto Galera through pipes...and the Philippines is a tropical and sometimes hot country. Natives will tell you that there is nothing to worry about and they don't have to, but people from other elsewhere might not always agree. If you are not sure whether your intestines agree, bottled water is readily available and it could highly contribute to an enjoyable vacation. Avoiding ice cubes and handmade ice-cream could be a wise decision as well.
Food preparation is generally to a lower sanitation level than people are used to in more affluent countries. Does this make eating unsafe? Absolutely not! Bigger resorts and hotels generally have a very acceptable standard, but whether you decide to eat in a smaller or bigger establishment, as a rule of thumb, when the establishment looks well-maintained and clean, it usually is.