When it rain's water comes from around the heater vent on to the floor. What do I do to fix this?

YOU find out where the water is getting into the heater vent in the first place and correct that.

Since heaters are usually located indoors... you are going to need to get a professional to find out how the water is getting there in the first place.

Water should NEVER be in the heater vent as it will breed all kind of bacteria and mold.

If this is the main heater vent pipe, the weather boot and or cap is separated and needs to be caulked or replaced.