Many times a beginner does not know if he or she wants plants and fish so this basic design allows for either situation. The line in the middle is a shelf which in this case would start off at 18 inches and go to 12 inches to the right where there will also be a skimmer. The shelf can be placed anywhere depending on how much you want plant material.
In this case the planting area would be a little over 50 percent of the length. Now here is the rub. We all know that as koi get bigger they tend to destroy plants. They will root around in the mud in the containers and tip them over. In the spring they will eat the tender new growth before it has a chance to get started.
In our situation above we build a stone wall across at the line where the shelf is. We put it together with cement on top of the liner (which in turn is on a footing to avoid collapsing). We want this wall to be stable so we use cement. In this wall we leave out a number of strategic stones that allow rather large fish to swim from deep to shallow. As the fish get larger, we refill those openings with the original stones simply to plug the holes so the larger fish can not have access to the plant side of the pond. Since we have the original holes where these stones would have gone, we simply use the original stone and place it in the hole. Meanwhile there are other openings throughout the wall that are small and will let water flow through to the skimmer.
The height of the wall should be about an inch lower than the water level. If you end up with fish that want to jump over the wall then you can build the wall higher. This can be done during original consecution or possibly by laying stones on the wall at a later date. Make sure you make the wall wide enough at the top to place another course of stone. In finishing the wall it is a good idea to use cement at the bottom of the wall sloped out from the wall to create a place for debris to stop. It will be much easier to clean up trash on the bottom of the pond if it does not go under irregular rocks.
A view from the side
When we are starting with a clean plate, I like to draw out the pond outline on the ground. We then did a trench all the way around the pond 12 inches deep. After we assure that it is level, we drive small pencil sized sticks in the ground so that two inches sticks up above the soil. Usually we use some rebar in these trenches and then fill to the top of the sticks. This gives us a flat surface to stack stone on. We will stack it at lease 10 inches high which would be the water level but it can go higher.
What this means is that when someone is looking in the pond and sees the stone neatly stacked, depth perception creates an impression of the stone going much deeper into the water if not all the way to the bottom. In time the liner and stone will both have algae grow on them which helps the illusion.
In the diagram below there are a couple of other issues to mention.

The footing adds strength to the entire project and keeps the top of the walls from collapseing. If you anticipate that you would like to have some larger boulders at certain places around the pond, the footing can be made wider and thicker.
The bottom drain is four inches. I have seen little koi 3 inches long swim down into a 4 inch drain and swim back out. If the pipe is smaller, the suction can be so much that fish will readily be drawn into the drain and either end up in your filter or clog up something.
The pipe leading from the bottom drain should go all the way outside the pond before it makes any bend upward to a vortex or other device. The pipe should be level or possibly slightly downhill so that debris will not become trapped in the pipe under the pond. Once outside the pond use 45% or 22% elbows to get the water back uphill. 90% elbows will surely cause you problems.
Do not use inexpensive drain pipe but use schedule 40. Once outside the pond itself, I downsize to three inches and from there go directly into a vortex chamber.
Depth of the water
I like for a koi to be four feet deep at the deepest point although I have used three and one half feet which has always worked out well. If the bottom slopes toward the bottom drain you will have a very hard time walking on it. Once you go up above the shelf, the pond slopes from about 18 inches to 12 inches at the shallow end. This is gradual and you will be able to place plant containers on it. Water lilies like 16 to 18 inches of water and some will do well in 12 inches. Other plants in containers can also be placed on the shelves.
More later. 07132009
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