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Welcome Northershore!  Yep most streams this time of year are running low because alot of the streams rely on rainwater to sustain good flows, so the streams on the Northshore fluctuate quite a bit.  The Cloquet does to some extent, but its part of the Minnesota Power hydro electric water areas and doesn't flucuate as much.

The Cloquet river is a fantastic river for smallies, some northerns and an occasional brook or brown trout.  The problem is the limited public access to the river and it's not which you call an easily wadeable stream for fly fishing.  The only place I have done some smallmouth fishing is area right below the Island Lake Dam.  There is a public access area to Island Lake right at the dam and then you can take a trail heading down to the area behind the damn.  I have only been there a couple of times and did catch some small smallmouth, but know of others that fish in that area for smallmouth and walleyes.

The Cloquet river is perfect for drifting, either by canoe or pontoon floats.  John from Great Lakes Fly Company, located in downtown Duluth, fishes the Cloquet river quite a bit on pontoons, guiding clients.  I'll be going with him before the months end to try out one of his pontoon floats and fly fish the Cloquet in the lower sections.  I've fished the lower sections of the Cloquet by 14' boat, but mainly for walleyes and we'd catch quite a few smallmouth as well, but I wasn't into alot of fly fishing back then.  I was actually just there yesterday on a little drive and scouting out the river.  The river just screams smallmouth river!  It's looks like right now, the smallies would be looking up at hoppers!

Northshore you should come out with me on the St. Louis River.  This past week I actually got up early enough to get in a couple hours fishing before heading to work on the St. Louis River.  I really just wanted to see how the bass fishing was in the morning with all this hot weather we've been getting in Duluth.  In the couple of areas we fished, the fish were stacked up shallow and just off the first edge of rocky shorelines.  Fortunetly I didn't bring my fly rod, cause I was just mainly doing some scouting.  So now I know where to go with my fly rod.

Good luck out there and be safe.