We're planning to go to St.Louis then to the Ozark or Ouachita area. We would like to stay in a wilderness lodge or cabins close to hiking trails and water (rivers or lakes). Does anyone have lodging recommendations or advice on trails we shouldn't miss?

I live in Hot Springs Village in the Ouachita Mountains. You might try Lake Ouachita State Park for cabins, or you could rent a house here in the Village and go hiking in the nearby Ouachita National Forest, which has many great trails. There aren't many rental cabins by Lake Ouachita as it is in the national forest.

This website has all the Arkansas State Parks with cabins, etc..
http://www.arkansasstateparks.com/
Also, there are nice cabins to rent in both Eureka Springs and Branson. A search will reveal many options in these two areas.

From St. Louis, I would head down past Taum Sauk Mountain to the Current and Jacks Fork River areas, around Eminence, Van Buren and thereabouts.
http://www.currentriver.net/
It's my favorite part of the Ozarks, which I've been going to since I was a kid.
If you wanted to head west after that, take US 160 west. Beautiful road.

Reading your question again, I'm wondering if you really mean to go to the Ouachitas from St. Louis--it's a good day's drive. But Arkansas has the most beautiful state parks, so I would recommend you take japw82's advice and go to the website for more information.

Try the Sugar Ridge Resort. I haven't stayed there but have heard wonderful things about it.
http://www.eureka-net.com/sugarridge/

Thanks for the great advice. We will be driving to St. Lous from Georgia and will stay there a couple of nights then drive to the Ozarks. We haven't decided where to stay there yet but thanks for the recommendations, happytourist and bbgboy. Then we plan to drive down Route 7, which is supposed to be beautiful, to stay a couple of nights at Mount Nebo State Park. It looks truly beautiful on the web site. It was very hard deciding on a park to stay at since there are so many great ones. Thanks for the tip, japw82.

agree with BBqboy that area around Eminence, Lesterville, Ironton is wonderful- and very uncommercialized.
Also he didnt mention the Black River - another favorite. There is Wilderness Lodge on the Black River close to Lesterville and also I believe Black River Lodge.
If you have kids along, Elephant Rocks is a great place to visit as well as Johnson ShutIns ( which may be flood damaged due to break in Taum Sauk damn.
Its a great part of the country and I miss it- live in Oregon now