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Pond design is divided into three categories: 1) Aesthetics, 2) Structual and Mechanical Integrity, 3) Proper Water Quality. To acheive the ponds full potential, all three aspects must be met in complete unity.
Aesthetics: Designing the pond to look just as expected, Beautiful! Making sure the pond follows its given theme, natural or formal. This aspect of design is something a good pond installer can see before hand through precise visualization. Pond & Landscape is proudly claiming the most attractive work.
Structural and Mechanical Integrity: Designing the pond to be properly and securely built. This includes the excavation process, liner or concrete installation, all existing plumbing and filtration systems, and especially rock work (making sure that all stones are tight and secure with no chance of wobbling, tipping or falling apart into the pond). Leak prevention is a very important part design. Leaks can be found in both plumbling and the more common, poor rock work. The professional pond installer takes his time to make sure this is not an issue.
Proper Water quality: This aspect of design is the most overlooked - Designing the pond so that the actual structure of the pond does not adversely affect pond water quality. Such as the proper location of stones and gravel as well as the necessary promotion of beneficial bacteria colonization found in a proper filter system. Water quality is the most important part of design. Below are the improper and proper methods as well as a precise description of the nitrifying cycle.
Improper Method: Building a pond with stone and/or gravel on the bottom.
Stone is to be used around the perimeter of the pond and in the rock shelf where marginal plants will be planted. Small boulders tapering down the sides are fine in a water garden but not in a Koi pond. Koi, when larger, can easily scrape or swim into these rocks causing injuries that could get infected. Smaller fish do not seem to have this problem.
Gravel or river stone at the bottom of the pond is much worse. Many installers are claiming that beneficial bacteria (explained in "nitrifying cycle") will grow in this gravel and help the pond. Nothing can be further from the truth. Sediment or “detritus” in the pond will settle to the bottom working its way into the gravel. Detritus consists of fish waste, uneaten fish food, dead plant material, and all existing organic matter. Since there is no movement or circulation "through" this gravel it becomes stagnant and anaerobic (non - oxygenated). Toxic bacteria such as aeromonas or pseudomonas bacteria will now grow in this gravel. The by product from this bacteria and muck existing in the gravel will create poor water quality. Examples of this will create abnormal increases in ammonia and nitrites, as well as parasite infestation and excessive algae blooms (green water). Eventually a methane gas called hydrogen sulfide, a deadly gas that will easily kill the fish in the pond, will exist. Bacteria additives are sold to the pond owner on a consistent basis to break down this sludge. This sludge can not be completely broken down regardless of any additives and will eventually need to be removed. All the bacteria the pond requires already exist in a proper filter system. Here are the affects of gravel and river stone in the bottom of a pond.

White marshy muck!
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Watery sludge in gravel
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Gravel removed before rinsing pond
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Proper Method:
Removing or never installing gravel will prevent the toxicity problem from occurring. This will allow more water volume to exist (the rocks take up mass that water cannot occupy in the pond) as well as increasing overall pond circulation. This allows the pond owner to stock the pond with more fish. With a bottom drain, submersible pump, or maintenance vacuuming, the pond bottom can stay clean. The gravel present in the rock shelf area is not “anaerobic” because the roots of the marginal plants keep the gravel aerated through their movement and growth. These plants also eat all the nutrients (caused by organic debris) present in the rock shelf, thereby cleaning it. Ponds that have a clean bottom will actually look better than a gravel bottom because Koi are meant to be viewed over an opaque or non reflective surface to bring out their colors. A bare liner will create this view. A “beneficial” black algae slime will eventually coat everything in the pond including the rocks, thereby loosing the stones aesthetic value. In short, the pond acquires a black look anyway. This design is much more natural looking because it will actually create the illusion of an undetectable depth or “bottomless” view to the pond, making it look absolutely outstanding.

Before Removing Gravel...
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Watery sludge in gravel
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Koi in a proper design...
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Nitrifying Cycle:
This is a must know for every pond owner. The nitrifying cycle is how nitrifying bacteria comes into existence in the pond and helps us. For without it no pond could ever exist. It needs four requirements: (1) Food / ammonia (2) temp. 55 degrees – 85 degrees F (3) Area to colonize and live / filter media (4) high levels of oxygen.
Fish create ammonia (NH3) primarily through their gill respiration and through their waste. Ammonia is also created by any other organic matter such as fish food, leaves, decomposing plant life and all other debris. Nitrosomonas is the first bacteria that will convert ammonia to its next available form known as nitrites (NO3). Nitrites is a derivative of ammonia and is still very toxic to fish. Nitrobacter, the second bacteria to exist, will break down these nitrites to its next available form which is nitrates. Nitrates (N02) are available plant food for aquatic plants and is not harmful to fish even in relatively high levels. Aquatic plants consume nitrates, consequently cleaning the water of all pollutants. All of this takes place inside a properly built biological filter. Without this miracle of nature your pond has no chance for success.
Here are some visuals of some designs:
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