In the water heater closet, the water heater is vented through the roof. There is a vent pipe that goes through the floor in the same closet. What would this vent pipe be for and can I cap it off as I have mice and I think they are coming in through here. I also have a tremendous amount of lint build up and I'm wondering if it's drawing lint from the dryer through it.
If it's a gas water heater, it could be a combustion air intake. Without it, the heater will not have enough oxygen to maintain a flame.
You should be able to prevent mice from entering the vent, by covering it with a grate, grill, or screen.
As for lint being drawn in, it sounds like you have to investigate how the dryer is vented.