I went to go fish when I saw two zombie villagers underwater, initially I thought that it was a bug that affect zombie villager to not be able to swim not suffocate underwater.

Upon jumping into the water to kill them I found they were in an air pocket, a quick F3 confirmed we were in a new Marsh Biome and mobs were spawning underwater unable to reach the surface, this marsh biome was located within a desert while running large biomes.

any lake and or pond over 3 blocks deep had this effect.