This is an old debate. Both sides of the argument seem well entrenched with little or no movement. The debates have been very heated and at times gotten out of control. My purpose with this article is not to fan any flames, but instead to give my own opinion on the matter. So please keep the hate mail to yourself.
It is this author’s opinion that rocks have no place in a true koi pond. Rocks will trap debris and create a breeding ground for parasites and bacteria. If left unchecked it will eventually create a highly toxic environment and claim the lives of your koi.
Now, before you start throwing water balloons filled with fish mulm at me read the above statement closely..."If left unchecked..." This means that if those rocks are never cleaned out you will create that "toxic environment". BUT, if you are willing to put the work into cleaning and maintaining the rocks then it is possible to keep koi healthy and happy in a rock bottom pond. How much work are we talking about? Well at the very least an annual drain and power wash. Bi-annual would be even better. But this is a messy and difficult task and it’s expensive to hire a professional to do this. So far too often this goes undone and after a couple years the fish start to die.
Now I would like to go a further with this discussion and talk about the different types of koi ponds. Before you decide if you want rocks you have to ask yourself what you want from your koi and your pond. If your intent is to raise high quality koi for show or at least to raise high end koi to their full potential, then rocks are not something you should consider. A smooth bottom pond will make it far easier to provide the ideal conditions high end koi require. Even with frequent cleanings, the rocks will trap debris and increase the dissolved Organic Compounds (DOCs) in the pond. This trapped debris will prevent the koi from reaching their full potential. Colors will fade sooner, their whites will yellow and so will their heads. Their skin will lose that prized luster and they will not grow as big. In other words, while they may survive, they will not thrive.
On the other hand, if you have no intention of ever showing or even purchasing high end koi and you are more interested in a beautiful pond with some nice koi and you are not concerned with developing the koi to their "maximum potential", then rocks might not be a bad decision. Just keep in mind the facts above about the annual cleaning. This is REQUIRED for all rock bottom ponds. If you are not up to the task, then don’t put in rocks.
Another thing to consider when adding rocks to the bottom of your pond is how the water will get to the filter. If the only method of sending water to the filter is a skimmer, you will vastly compound the problems with rock bottom ponds. With a skimmer only set up, all the sinking debris and waste produced by the fish will remain in the pond. 90% of all fish waste will sink below the skimmer line. If you decide you want rocks on the bottom of the pond, you need to consider some sort of bottom drain under the rocks. This can be done a number of ways, but what is really important is that sinking debris will at least have a chance at getting to the filter. With a skimmer only situation there is zero chance the waste will ever make it into the filter system. The water will become toxic much faster and rocks will need to be cleaned more frequently.
Before I end this discussion there is one myth I would like to discuss about rock bottom ponds. Many will tell you that the rocks will become a bio filter for the pond and it will convert that fish waste all on its own. Let me say right here and now that this not true. Anybody who says different has very little understanding of how the bacteria in a bio filter really works. While at first some beneficial bacteria will form on these rocks, they will quickly be choked out by all the fish waste that is allowed to settle there. This is the reason we install mechanical filtration before our bio filter. We do not want any of the fish waste and debris to clog our bio media.
So should you put rocks in your pond? Only you can answer that. I know of many ponders who have raised healthy beautiful koi for many years in a rock bottom koi pond. And should you decide to add rocks, below are a few tips to consider:
1) Use larger rocks and only place them one layer deep. Pea gravel will be impossible to clean.
2) Use smooth river rock so debris will not be trapped as easily.
3) Install a bottom drain at the deepest point and leave several feet around the drain smooth and free of rocks.
4) Install several TPR’s or underwater jets to circulate the water and prevent debris from settling.
5) Invest in a good pond vacuum and frequently vacuum over the rocks to remove as much debris as possible.
6) Consider the option of mortaring in the rocks. This way you have the look you want, but a smooth enough base so that debris won’t get trapped under the stones.
7) Consider a smooth bottom pond with a couple pebble/rock beach areas near the edge. This way you have the look of rock with the benefit of a smooth bottom.
8) Keep the stocking density LOW. Rock bottom ponds cannot hold as many koi as a smooth bottom pond.