From your description, it seems you were up the Lower Moon River heading to Moon Falls. Yes, there can be a substantial current in that stretch, especially in spring. And yes, Walleye do come in there...that's why it's a sanctuary.
There are more subtle currents throughout the archipelago, in neck down areas and channels between the islands. G Bay experiences a phenomena called a "seiche"...it's like a freshwater tide caused by the wind. A prolonged west blow can temporarily raise the water level by over a foot, a prolonged east blow can drop the level the same amount. All this water rushes in and out of the myriad of channels creating current areas...these spots attract predators feeding on the baitfish (in turn attracted by zooplankton) being swept by.
If I can give you two pieces of advice....First, journey out and away from the Lower Moon and Woods Bay...it gets pounded. The further you get from the marinas and launches, the better the fishing. Those reefs out by the outer band of islands always have consistently good fishing..On a calm day, go out even further to those offshore reefs...few complaints about slow fishing out there..
Second, a lot of the reefs/structure is smooth featureless worn rock...ignore those. Look for structure that has broken rock, preferably boulders of between softball to basketball size...if there's cabbage weed nearby, even better...
Enjoy....there's enough fishing and places to explore in that area to fill several lifetimes.