Keywords: Koi, Goldfish & Pond Health - Nitrates - Final by product of the Cycle in Koi ponds and water gardens and major contributor to green water or Algae blooms.
All research done on Nitrate in the pond shows that it's not toxic to the fish on the short term. On the long term, high nitrate levels (> 80 ppm) will cause a depressed immune system, zero reproductive capacity, red veins appearing in the fins, and slowed growth. Nitrate is made from Nitrite by naturally occurring, beneficial nitrogen reducing bacteria. Plants and algae use nitrate. Ponds with a lot of plant or algae growth typically will have Nitrates under natural control. Nitrates can be reduced with water changes, reduced feeding, and plant deployment. It is NOT advisable to clean the bottom of your pond spotlessly clean of algae. The algae, in proper amounts, are an effective nitrate reducer.
Additional Reading on Nitrates by Dr. Erik Johnson (The longer article)