Significantly different. From what I understand, Librefox intends to follow upstream development with limited changes. Waterfox, on the other hand, is a fork of the pre-XUL, pre-Electrolysis Firefox circa 2017. As upstream development continues, it will become increasingly difficult to maintain these sorts of forks.

waterfox is a complete browser based on an old version of the firefox engine. This project is a set of dot files that setups current mainline firefox.