Welcome to the forum! The fact that the creek bed is DRY, makes me think your pond builder is wrong. I would definitely put down a well compacted clay liner over all the exposed rock. Ask your "pond builder how he intends to compact the soils also...if they say the track equipment is heavy and compacts it, they are wrong! Tracks are wide, they float with minimal compaction. Require a sheepsfoot roller be used, or a wheeled earthmover.
Osage County is the northern edge of the Ozarks where lots of limestone and sandstone grows better than most plants. It takes some pond building skill and/or someone with knowledge supervising a good dirt mover to build a pond properly in your area. Many dirt pushers get lucky building some small ponds, but will never tell you about the dozens there that never held water.
