A possible nutrient source is wastewater from the treatment of sewage, agricultural, or flood plain run-off, all currently major pollutants and health risks. However, this waste water cannot feed algae directly and must first be processed by bacteria, through anaerobic digestion. If waste water is not processed before it reaches the algae, it will contaminate the algae in the reactor, and at the very least, kill much of the desired algae strain. In biogas facilities, organic waste is often converted to a mixture of carbon dioxide, methane, and organic fertilizer. Organic fertilizer that comes out of the digester is liquid, and nearly suitable for algae growth, but it must first be cleaned and sterilized.
The utilization of wastewater and ocean water instead of freshwater is strongly advocated due to the continuing depletion of freshwater resources. However, heavy metals, trace metals, and other contaminants in wastewater can decrease the ability of cells to produce lipids biosynthetically and also impact various other workings in the machinery of cells. The same is true for ocean water, but the contaminants are found in different concentrations. Thus, agricultural-grade fertilizer is the preferred source of nutrients, but heavy metals are again a problem, especially for strains of algae that are susceptible to these metals. In open pond systems the use of strains of algae that can deal with high concentrations of heavy metals could prevent other organisms from infesting these systems. In some instances it has even been shown that strains of algae can remove over 90% of nickel and zinc from industrial wastewater in relatively short periods of time.