Brad, you need to do some testing on small areas to know just what you are dealing with before proceeding.
Water marks from tap water or well water are not quite the same as those from water that has traveled through who knows what, in the roof.
Sometimes water coming thru a roof contains some oils or asphalt, etc and will need some kind of solvent.
Wet out a square inch area and agitate to look for foam or excess soap residue that could interfere with the removal process if not rinsed out first.
Then clean a small area 3' x 3' with your regular pre-spray using a spotting machine - check what comes out.
Cleaning will do nothing to remove water marks or rust but will let you know what else lies in the carpet.
Towel off and speed dry with a fan. This is similar to using an OP machine with a cotton Pad.
Once dry if the test cleaned area really looks different or lots of residue came out, you will have to explain the facts to the customer.
Spray another area with 9% Peroxide - do NOT add ammonia for this - it is the best and fastest solution for water marks but not rust.
You can do another test area with an encap product as a comparison.
Rust marks should have a definite shape of the metal object that caused it. If it's just on the edge of large stain it is just a concentrated water mark usually found at the last place that the water
For heavy water marks, you will need to towel off the peroxide after a few minutes ( absorbing some of the minerals like iron oxide that are the visible element of a water mark) stand on the towel and then re-spray with some more peroxide and leave it to work.
Also, test a couple of rust removers on some areas.