Alton, Illinois? If so...
There are many caves, including some significant ones, in Monroe County, a little to the south, and MO has many caves, including the famous one in Hannibal, to your NW. So you are certainly in an area where caves are feasible geologically. You seem to be describing a natural cave to me. Is the limestone thin-bedded, (are there many horizontal cracks in the cliff face, how far apart are they)?
If you can get some specific coordinates to me via PM, I can track down local cavers who will be able to provide any known background on this site.
But it will be more interesting and informative for you to simply explore the cave yourself. Be careful not to hurt yourself or the cave. Helmets are good to protect from bumps and falls, but moving slowly and carefully is the best way to stay safe. Since there is an active stream, look for signs of flooding, and avoid getting too deep when rain is forecast. Other than that, caving is mostly commonsense stuff.
If you're in one of the UK Altons, sorry to have rambled, but the last paragraph still applies.
Enjoy your explorations!