Ocean water causes dehydration, i imagine the pumps are for filling up the aquarium or just bilge pumps to keep The Ark afloat. They probably do desalinate ocean-water (wouldn't want to rely on rainwater), but it wouldn't be a part of the aquarium, and it would always be running, those pumps aren't in use.
If you were dying of thirst from lack of enough water I'm sure you'd drink ocean water.