As long as the waterfall is present, your villager will not see or be able to pick up the keystone from the beach.

As soon as the stream up top has been 100% cleared of debris, the water will flow down the stream and around the tree, and the waterfall will disappear. That's when you need to drag your villager, who is adept in both Building and Research, down to the beach where the waterfall used to hit the sand (see attached image). Drop them on the v-shaped rock that should now visible (the keystone) and they should pick it up and take it to where it needs to go.