Have you considered exploring the storm drain system?
I've been doing some thinking; if any particular part of the drainage system was built before or during the use of the Fredericton Underground, then there's a decent chance that there would have been some connections made between the two. Also, if there are connections inside the drains, these are about the least likely of the connections to have actually been sealed.
Part of this is because the tunnel still might need to have drainage for one reason or another, and second because they probably would never expect anyone to delve that deep into the storm drains anyway, thus making it not really a risk for them.
I took a look on Google Earth for a possible drainage infall and found this(the infall position is circled in red):
I can't tell if it's water or not, but it seems like the only obvious water source in the city, and the outfall would of course end in the river. Just about any course from that spot on the map toward the river would have to run past the Underground.
In any case, I'm strongly considering taking a look at some point.