What a cheerful name! It sounds as though it should belong to some sort of sprite or nymph.
The records do not specifically say whether Waters Merry was a man or a woman. I am inclined to think that he was a man because his name appears as the sponsoring parent at his daughter Rebecca's baptism at the First Church of Boston (Dec. 18, 1636). While it is true that mothers are often listed as the sponsoring parent when they were church members, this tends to be the case later in the century. In the 1636 records, all of the other children who are listed with a single parent are listed with their fathers. This doesn't mean that Waters Merry was necessarily a man, but I'm leaning in that direction.