Great thanks Colin, and I believe there are rainbow trout in the stream, and will only be taking 1-2 small rocks, and avoid disturbing any wildlife or habitats.I would if there were fish and shrimp in the stream. They would indicate the water is pretty clean and hasn't been poisoned, so the rocks should be safe. Just hose them off and leave in the sun for a few days, then add them to the tank.
Maybe put some more rocks in the creek to make up for the ones you remove.