More info will be needed in order to give you a proper reply.
is this a main return duct or is it panning (joist lining)?
is there a water pipe within this return?
Is the duct near a humidifier?
how much water are we talking about?
Does the duct end at an outside wall cavity?
I assume that this is an underground duct. You need a pump to remove the water. HOW the water got in there requires some investigation, because there are MANY ways it could have happened, not all of them serious.