Why would one battery of 3 be very low on water?

Take a picture of the wiring on your three 6 volt batteries in your rig, and post them up here, so none of us speculate what you've done.

Because it sounds like you have two left shoes and one right shoe, and you expect the electrical load to be balanced between all three... it isn't. To be balanced when 6V batteries are wired in series for a 12V system, you need an even number of 6V batteries, not an odd number.