Rust coming through on my pool waterfall - repair suggestions?

I take it that’s a concrete construction and not real stone. If so, then the likely cause is the rebar or reinforcing mesh is near the surface there and the rust is coming through. Only option is to chip it out, cut back the rebar or mesh, and seal it back up with cement. However, you need a pro with lots of experience and skill to do that or else the patch will stick out like a sore thumb. Matching color and texture of old concrete to a new patch takes a good eye for detail.