If it is river born of natural circumstance, I am sure there are brookies throughout the stream. Nature rarely lets any habitat go to waste. For example, let's say an earthquake formed that place one thousand years ago. At that time perhaps a natural dam allowed fish to escape only in to the lower part from a tributary nearby. Over the seasons, an osprey might hunt the lower river and occasionally drop its catch in the upper and so on. "Nature finds a way."
As far as scaling waterfalls, salmonoids actually use the force of the downstream current to push off with their tails, exactly like a tacking sailboat. They can scale impressive heights. Even in a large waterfall there may be smaller places to swim vertically. "Nature finds a way."