The effect of nitrate on the aquarium and pond system has not been very well understood in the hobby over the years. In fact, it was often considered harmless. We now know it is not harmless and is the most likely cause of Hole in the Head (HITH) disease in cichlids and Head and Lateral Line Erosion (HLLE) in Marine fish. In aquatic science, it is often called chronic ulcerative dermatopathy or chronic erosive dermatopathy. Death can eventually occur if nitrate remains unchecked in the system.
First, a review of how nitrate accumulates in the aquarium. In general, fish excrete ammonia through their gills and waste. Ammonia is then oxidized by Nitrosospira and Nitrosomonas bacteria into nitrite, and then Nitrospira bacteria oxidize nitrite into nitrate. In most hobbyist aquariums, nitrate accumulates over time, depending on the bio-load and any nitrate-reducing systems that have been implemented.
Very little, if any, research on the effects of nitrate in the aquarium or pond system has been conducted. Most of what we know about the effects of nitrate is through long-term observations by advanced hobbyists.
Some research has been conducted on nitrate with cattle and humans, and because of this research, the Environmental Protection Agency has set the Maximum Contaminant Level (MCL) for drinking water at 10 ppm.
When consumed by human infants and cattle, anaerobic bacteria convert nitrate into nitrite in the digestive tract. The red blood cells adsorb nitrite in the digestive tract, displacing oxygen and creating Methemoglobin.
Methemoglobin turns the blood brown because it is no longer carrying oxygen. This condition is known as methemoglobinemia. If nitrate ingestion is not discontinued, suffocation (death) will occur.
In my experience working with aquariums and troubleshooting aquarium problems for other hobbyists, excessive nitrate in the aquarium is the cause of Hole in the Head disease in cichlids, and Head and Lateral Line Erosion in Marine fish. In every case, I have worked with, high nitrate, often over 400 ppm, was present.
Hole in the Head, and Head and Lateral Line Erosion has been suggested to be caused by a lack of vitamins, poor nutrition, stray voltage, use of activated carbon, and internal parasites (Spironucleus [Hexamita]).
In cases where fish had proper nutrition, the aquarium had no stray voltage, and did not use activated carbon in the filtration system, fish still developed HLLE in high nitrate water.
In cases of cichlids, I have donated lots of apparently healthy and unhealthy discus for fish disease research, and in most cases, both healthy and unhealthy fish had Spironucleus in the digestive tract but never exhibited HITH.
In my experience, it is possible to reverse Marine Fish HLLE by moving the fish to a system with less than 40 ppm nitrate. I have been able to reverse the condition in clownfish (A. ocellaris), and several species of tangs. The process can take months, depending on the species, but it can also completely reverse the condition.
How does nitrate cause the HLLE and HITH? Based on what we know about the nitrate research on other animals, the Griffitts hypothesis on nitrate toxicity in fish works like this:
Nitrate also has an adverse effect on reef invertebrates, especially clownfish host anemones. Many fish breeders have noticed nitrate can be a growth inhibitor and stop reproduction.
When maintaining an aquarium or pond, it is recommended that you keep the nitrate level below 100 ppm for a fish-only system, below 40 ppm for most reef tanks, and below 20 ppm for systems that house host anemones.
There are several methods of controlling nitrate:
A denitrator uses anaerobic bacteria to reduce nitrate to nitrite and then to nitrogen gas. It works by flowing water slowly through a filter with a lot of surface area for bacteria to colonize. Aerobic bacteria near the front of the filter use up the oxygen in the water, creating an environment for anaerobic bacteria to do their work, reducing nitrate.
Deep sand beds in marine systems help reduce nitrate by allowing anaerobic bacteria to colonize. Spaghetti worms (tube worms) and other invertebrates that colonize the sand bed help exchange water slowly through the sand bed enabling anaerobic bacteria to reduce nitrate to nitrogen gas. Generally, you need a 2-inch (5 cm) fine sand bed to see some de-nitrification.
Macro algae and aquatic plants take up nitrate as a nutrient. Many reef aquarists use macro algae in a refugium to take up excess nitrate. Reef systems that have macro algae often have an undetectable nitrate reading. Heavily planted aquariums with bright light can also help control nitrate. Ponds with lilies, cattails, and other aquatic plants that get a lot of sunlight often have an undetectable nitrate level, even when heavily stocked with large koi.
Water changes must occur when nitrate accumulates in the system over time to reduce the nitrate level. How fast nitrate accumulates in the system will determine how much and how often water changes need to be done. In some cases, near 100% water changes may need to be done monthly or more often to keep nitrate within safe levels. Large percentage (90% or more) water changes are perfectly safe as long as the new water's pH, salinity, and temperature are close to what is in the system.
There are many products on the market that claim to reduce nitrate. Some are liquid chemicals, and mineral rocks like zeolite. None of the products I have ever tested worked as claimed. If nitrate reduction was accomplished with these products, it was so small it could not be detected.
Keeping nitrate in check is crucial to long-term success with an aquarium or pond system. Test your system periodically for nitrate, and establish a water change schedule to keep nitrate below acceptable levels. Long-term fish health depends on you maintaining a low nitrate level.
Since the original publication (2007) of this article, research published in 2020 shows a direct relationship between nitrate and methemoglobin:
Daniel F Gomez Isaza, Rebecca L Cramp, Craig E Franklin, Simultaneous exposure to nitrate and low pH reduces the blood oxygen-carrying capacity and functional performance of a freshwater fish, Conservation Physiology, Volume 8, Issue 1, 2020, coz092, https://doi.org/10.1093/conphys/coz092