A number of places will have indoor pools, though I don't know of any that really merit an "indoor waterpark" description. About halfway between Macon and Valdosta, the Fairfield Inn in Cordele has an indoor pool and is very nice, modern and well-kept (and just a few years old). We stayed here about a month ago.
The Comfort Suites in Byron, Georgia (maybe 10-15 miles south of Macon?) also has an indoor pool and is very nice as well. In Valdosta, I'd go for the Country Inn & Suites, which also has an indoor pool. All three of the above offer free breakfast.