Mechanical and biological filtration are critical to processing the many types of nutrients found in a pond ecosystem, including fish waste, uneaten fish food, leaves, and runoff from lawns to name a few. High levels of ammonia (a form of nitrogen) are highly toxic to fish and are a major contributor to prolific algae growth, and so they need to be carefully controlled. In water gardening, the primary nutrient that biological filtration utilizes and renders usable is nitrogen.
In biological filtration, nitrifying bacteria, known as facultative bacteria, absorb ammonia, and turn nitrites into nitrates, which are less dangerous. These bacteria require oxygen to live, so it’s important for the pond’s pump to run 24 hours a day, 7 days a week. If the pump isn’t running, the waterfalls aren’t flowing, and aeration is eliminated from the necessary equation to maintain an ecosystem pond. Keep in mind that if the pump shuts down, the bacteria will quickly use up all of the oxygen and die. This isn’t a good thing.
Nitrates are then removed from the pond by another biological filtration method known as de-nitrification. This process occurs only in anaerobic (without oxygen) areas of the pond. That’s why it’s not necessarily bad for some areas of the pond to experience minimal water flow (such as on the bottom of the pond, under an inch or so of gravel). The bacteria that live in this area of the pond turn nitrates into nitrogen gas, which is released into the atmosphere. Nitrates are also absorbed by aquatic plants and algae during their growth processes. A pond without aquatic plants will prove to be a maintenance nightmare.
For any biological filtration to work, there literally needs to be billions of bacteria working to purify the water. They prefer to anchor onto things, which is why surface area is so important. More surface area means more bacteria, and more bacteria means better biological filtration. Surface area is provided by filter media, rocks, and gravel. A pond with gravel on the bottom will contain more surface area for bacteria, as opposed to a pond with exposed liner on the bottom.