Directionfinder,
We were on the Inner loop itinerary just after Mary, late May into early June. Flora provides shorty wetsuits, masks and fins; these are fitted to each passenger on the first day and used throughout. We did just about every snorkeling excursion that was offered. The crew did not say that the water was cold, rather defined it as various degrees of "refreshing". Chilly when one first entered but after a minute, we were comfortable in the shorty suits. We were also told that the cooler Humboldt current arrived early this year and that the water was cooler than usual for May/June. Again, nothing that made us uncomfortable; we typically stayed in the water for up to 45 min on each excursion. One positive note is that the cooler waters meant more varied marine life. One one excursion, we were able to snorkel with a 10 foot manta ray. One last note; deep water snorkeling meant that you entered the water directly from the zodiac rather than from shore; don't expect to be able to stand with feet on the bottom; depths ranged from 10 - 40 feet.
There were multiple excursions offered each day; one could easily participate in three per day. If you didn't want to snorkel or take a long hike, shorter hiking options or zodiac rides were offered. As for the hikes and other land excursions, our daytime temperatures were in the low 70s. We wore shorts and short sleeve tops and were very comfortable. Just remember the hats and sunscreen and you shouldn't have to worry about burning.