GreenClean is an excellent fish-safe algaecide for string algae on rocks and streams. You will have to shut your stream off temporarily while you apply the product and allow it to work. A 2lb jar would run you about $25, but will last you quite a while, particularly if you are using it as a spot treatment.

Here is a link for more info: GreenClean Algaecide

Natural Environmental Systems pond supplies for environmentally friendly pond maintenance solutions