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Rocks on the Bottom of Your Pond: The Fallacy That's Making Your Koi Sick
Koi Health Blogs

Rocks on the Bottom of Your Pond: The Fallacy That's Making Your Koi Sick

by jason Kwalick on Jul 21, 2026

Let me ask you something. Did you ever have an aquarium when you were a kid? Or maybe you've got one right now sitting in the living room.

If you did, you remember the setup. You had that gravel on the bottom, those little colored pebbles or the sand, and underneath it you had one of those undergravel filters. The gravel sat right on top of it. And you remember what came next, right? You had that little siphon hose, and every so often you had to go in there and work that thing down into the gravel and suck up all the muck. All the crap. The fish poop. All that decaying material that settles down into the rocks. That was the deal. You couldn't just leave it in there. It had to come out, or the tank went bad.

Anybody who's ever kept an aquarium understands this. It's not complicated. Waste falls down, it gets trapped in the rock, and if you don't pull it out, it rots.

Here's the part that gets people. Somewhere along the way, that same person grows up, puts in a koi pond, and doesn't make the connection. They forget the lesson they already learned as a ten-year-old with a fish tank. Because the exact same thing is happening in their pond, just on a much bigger scale.

The rocks are the problem

You've got all these rocks in the bottom of your pond, and all they do is collect. Muck. Poop. Decaying organic material. And down in there, where the water doesn't move and the oxygen can't reach, you build up anaerobic bacteria and all that nasty stuff. That's not a nice place. That's a factory for the exact problems that put your fish in trouble.

And it's the same story with bogs. I know there are people out there who love their bog filters and their wetlands. They swear by them. They'll tell you it's the best thing you can put on a pond. It's not. A bog is a haven for bacteria buildup. It traps organics in a low-oxygen zone and just sits there and stews.

Look at what's going on out there lately. People are complaining left and right that their fish keep getting bacterial infections. Ulcers that won't heal. The same fish, the same problem, over and over, and they can't figure out why. Well, I can tell you why. You've got rocks in your pond. That's the main reason. You built yourself a bacteria machine and you're wondering why your koi keep getting sick.

Most of you don't even have real filtration

Here's the other piece of this, and it's a big one. Most of you don't even have real filtration. Be honest with yourself about what you've actually got. You've got rocks in the bottom of the pond, and a skimmer that runs into a little canister filter, and that canister pumps the water right back up to the top of a waterfall. That's it. That's the whole system.

So think about what that actually does. Everything you put in that pond, every pellet, every bit of waste, every leaf that blows in, settles down to the bottom. And it stays there. You can't even clean it out with a vacuum, because the bottom is full of rock. The muck works its way down into the rocks, into the crevices, into every little gap between them, and it just sits there where you can't reach it. And it builds up. And it builds up. And the bacteria builds up right along with it.

Now here's the part nobody wants to hear. It might be fine the first year. Might even be fine the second year. The pond's new, the rock's still clean, everything looks great. But go into year three, year four, year five. As that pond gets older, it gets dirtier. And the dirtier it gets, the more problems you're going to have. It's not a matter of if. It's a matter of when.

Follow the money

So where does all this come from? Why is everybody putting rock in the bottom of their ponds?

It comes from the pond builders. And I'll tell you straight, the pond builders make their money off selling you rock. That's it. That's the whole thing. That's why they came up with wetland filters and bog filters and every other fancy name they can dream up for a pile of gravel. Because that's where the money is.

Think about it. If a builder slaps a good bead filter on your pond, maybe he makes five hundred bucks. But if he sells you on rock, on a bog, on a "natural ecosystem," now he's making tens of thousands. So he's not going to sell you the bead filter. He's going to sell you the idea. He sells you a fallacy. He sells you a fantasy. He sells you something that isn't even true.

And here's the thing. Most of these pond guys don't even know the difference. I'm not saying they're bad people. Most of them aren't biologists. They're not aquaculturists. A lot of them are former pool guys, or plumbers, guys who know a little construction and can dig a hole and drop a liner in. And that's fine. There's nothing wrong with that. Somebody's got to build the thing.

But I'm going to stereotype for a second, and I'll own it. There are some big companies out there selling you a lifestyle. They build beautiful water features. Gorgeous stuff. But they don't build koi ponds. Because they don't understand koi husbandry. A pretty water feature and a healthy koi pond are two different animals, and most of these guys have never learned the difference.

So what do you do about it

The moral of the story is simple. Don't fall for the fallacy. Don't fall for the fantasy. Don't let these people sell you on something that's going to have you buying meds for the next ten years.

If you already have rocks in the bottom of your pond, my honest suggestion is to get them out. I'm not going to lie to you, that's a lot of work. Nobody wants to hear it. But those rocks are working against you every single day.

If you've got a bog filter on there, move it and get yourself a bead filter. Give your pond something that actually pulls waste out instead of trapping it.

And if you're not going to do either one of those, if you're going to keep the rocks and keep the bog, then you'd better be running potassium permanganate. PP. That's my Purple Magic, and you need to be using it once a month, like I tell everybody else to do. And with all that organic load sitting in your rock and your bog, you're probably going to have to run it a little hotter to keep up, because that muck is going to eat your PP fast.

It was never an ecosystem

Here's what it really comes down to. This whole "rocks and bogs are natural" thing is just another fallacy that the koi industry runs on. It gets people in trouble, and then what happens? You've got sick fish, so now you're buying meds. And more meds. And more stuff. It's a cycle, and it starts with rock in the bottom of your pond.

So let me tell you what your pond actually is. It's not an ecosystem. We are not building an ecosystem here. This is a fancy big fish tank. That's what it is. That's all it ever was. And the sooner you treat it like one, the healthier your koi are going to be.


Written by Jason Michael, a 30-year aquaculture professional with experience in commercial koi farming and fish health management.

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