Middle St Vrain is an awesome trail, but you shouldnt do it alone if you plan on doing Coney flats as well.
Those water holes are not very deep, I have had stock XJ's run through them easy, just got to take it slow, there is always rocks in all those puddles that snag shock mount and diffs. Those are two of my favorite trails.
SO you didn't go through the big water crossing (the water at the top of the hill?)
Highest it has been is like 3 feet.