The Flood - Animals and their minimum food requirement

By changing salinity or filling the water up with silt. Or changing its temperature. At least one of those three will kill most of the critters that live in water. And remember: if you kill the copepods and other such plankton, everything else starves.

Sure. And those pockets are full of cleanish sea water, not anoxic, silty, fresh-to-brackish water. A Floode that deposits the whole geologic column in under a year, like the one Faith wants, is not quite a newly-sunken boat.