A good safe product to use in your pond that cleans the pond, liner and rocks of algae etc. is Green Clean.  Green Clean Aquatic Algaecide works by oxidation and provides immediate control of string algae in ponds, fountains and other water features.  Within minutes you'll notice visible results.  It is safe and effective and is non-toxic to fish, aquatic plants and is biodegradable.  Green Clean works on contact to control algae (especially string algae) and is activated by water and safe for all animals once it is diluted in pond water.  It releases vital oxygen into the water as it biodegrades.  You want to keep the powder away from where birds or small animals can ingest it.  Again once diluted it is safe.  One pound (2 cups) of Green Clean treats about 4000 gallons.  It immediately begins fighting algae blooms.  Green Clean is safe for Koi and other pond fish and aquatic plants.  It is designed for ponds, lakes and other large bodies of water as well as for unpainted surfaces, such as docks and walkways.  Fast acting Green Clean biodegrades completely and adds 13% oxygen to the water.  A 2 lb. container of Green Clean will treat a 1,000 gallon pond for an entire season.  Results after application can be seen in 24 - 48 hours.  Green Clean has been tested and registered with the EPA.

Buy Green Clean here.