Backyard Aquaponics
A place to discuss aquaponics

I don't know if this is a cry for help, or just my last ditch effort to figure out what the hell is going on.

BACKGROUND: I've had my established backyard system going fine for TWO YEARS now. In those two years, I don't think I've ever lost a fish. So aquaponics isn't exactly new to me. My system consists of a 110 gallon tank and three 40-gallon grow beds filled with hydroton.



All of the sudden, roughly two weeks ago, fish began to die. Since the last 14 days, I've gone from 29 fish to about 8! Yes, you read that correctly.

The way it started was that I found about 6 dead ornamental fish (on the smaller side) all dead in the corner of the tank. Some were partially eaten so they may have been there a few days. Since I had so many fish though and never an issue, I hadn't been checking the water as much as I should.



So my first thought was, "Oh crap, was there some kind of ammonia/nitrite/nitrate spike? What could have killed them?" I checked all those levels with my test tube kit, and the only thing that appeared high was the ammonia (possibly 0.5ppm). Perhaps the ammonia was high because of the dead fish sitting in there, but more than likely, I think it began to slowly rise because all the fish were growing larger, and contributing more waste to the system. I think having 29 fish in a system with only 110-120 gallons of water is too much (but didn't seem like it when they were all babies).

But I digress.....

What could have killed them? I know.....perhaps it's because I had hadn't vacuumed out any fish sediment that may have been collecting around the pump inside the tank. You see, my pump cycles water from the tank to the grow beds, but inevitably, any solids that don't get sucked up sit around the sides and back of the pump. Well, there was a mountain of sediment in there.....so I used a wet-vac and sucked it up.

Thinking that would have some positive impact, I was surprised when more fish started dying.....this time, some healthy LARGE goldfish.



So I immediately went to the pet store with a sample of water, and had them test it. They said it looked fine, but the nitrates looked high. (NOTE: My nitrate readings at home looked fine, but the pet store used those little 5-on-1 test strips which indicated a high nitrate level. Strange, I thought.....possibly an error? I always heard those strips weren't that accurate.) Either way, they recommended a water change.

Now here is where I made my first big mistake. I did an aggressive water change (over 60% of the tank). My tank is about 100 gallons, by the way.

Up until this point, I've always just topped off water when it evaporated....never did a water change. Topping off always consisted of putting my hose into the tank and filling it until it was full (estimated about 10-30 gallons at any one top-off). Never did I ever put in any Stress Coat formula or Salt.


So after this drastic water change, within a few hours, I saw more "healthy" fish die. I believe that happened from shock: too much water changing places, and possibly a temperature difference from the hose?

A few days later, after it seemed under control, I started to see my Koi dying. All water tests appeared to be fine (pH, ammonia, nitrate, nitrite). The water temp was in the 70's or low 80's, and that's never been a problem. Always had good water flow and oxygen being returned from the siphons.

So like an idiot who means well, I decided on ANOTHER WATER CHANGE. This time, I took a bunch of 1 gallon plastic water bottles, filled them with water, let them sit IN THE TANK to get the temp acclimated, and then poured them in. I also added the right amount of Stress Coat formula and 1 ppt of salt.

I even built a new 15 gallon radial flow filter, to help collect any extra sediment from the fish bed and serve better filtration.

Despite all this, my fish are still dying (at least once per day).

I checked my ammonia and it appears a little high (between 0.25 - 0.5). I haven't fed the fish for 2 days now, and I have no idea why it's high. The only thing I can think of is perhaps the water changes from last week affected the nitrification cycle? What do you think?

Either way, I am totally helpless right now and have no idea what to do to stop the fish from dying. Any ideas?

First thing, salt to 3 PPT to help with any potential parasite or infection that you can't see.

Add more air, either by spraying water in or adding an air pump.

Then, check your ammonia, nitrites and pH...

If your pH is not around 7, begin VERY SLOWLY bringing it back toward there... By very slowly I mean less than .5 of a pH point per day.

These steps will help your fish reduce stress and also help with any ammonia cycle conversion and help your bacteria recover if your colony has crashed.

Other than this, not much else you can do. Avoid drastic changes. Your system is more likely to recover if you provide the right conditions rather than trying to fix non existent problems.

It sux, I recently lost 23 yearling silver perch. By the time I saw they were sick it was too late. But there was nothing more that I could do.

What the hell is eating your fish btw?

Thanks for the response! As for what's eating my fish, it's my fish! I have some larger koi in the system, and I think they are beating up on the smaller fish.

For example, I noticed a medium sized goldfish in a mild state of shock. I was easily able to pick him up out of the tank and move him into an isolated area of the system. However, before I did that, I noticed all the other fish brushing up against him and start to nibble at him. So hopefully, I saved him just in time. I think that in some of those pictures in my original post, once a fish was dead or defenseless, they were just picked apart by the larger fish.

Anyway, my pH right now looks to be around 7.8 or so, but I believe it's always been around that level (light blue on the test tube testing kit).

So you think that I perhaps disrupted the system's nitrification cycle from the drastic water change? I am thinking that may have been a factor in the ammonia spike......although I still have no idea what initially killed that first batch of fish unless it was just neglect on my part (ie not seeing a dead fish, which then raised ammonia, which then killed more, etc). The water change may have been a little too much.

Anyway, my system usually has 4 forceful streams of water creating bubbles in my tank (from the grow beds draining), so I believe it's getting plenty of oxygen. It's also moving the water well (since I have a 500 gph pump in my 150 gallon system).

I only hope that the ammonia comes down, and that whatever is killing my fish goes away.

One thing I have learned: from now on always do the following when adding new water:

- Add at least 1ppm salt
- Add Stress Coat to help with the tap water
- Only add water after it's the same temperature as the tank
- Never add more than 10-20% new water (or with changing water)

I really hope that resolves things. I feel horrible that after so much time, I'm down to only about 8 fish (I lost another big koi this morning).

With a pH up close to 8 and what I imagine might be reasonably high water temps still, those ammonia can be fairly toxic to fish..



See above, at 20 degree C and 8.0 pH ammonia levels can become toxic at around 0.53 for some fish species... While at the same temps, but with pH down around 6.8, you would need ammonia levels up around 8.0...

Another consideration, after two years your system may have built up a layer of goop in the bottom of the GB's that's turned anaerobic. In this case your pH would increase, as opposed to a healthy system where the pH is constantly dropping. You may also start to get Ammonia readings from a system/stocking rate that's previously managed to take care of the Ammonia.

If you do have an anaerobic layer of sludge and it's disrupted you will more than likely get sudden fish deaths. I had a customer that did this recently, he had a system that had been running well for 3 years, but the pH started climbing dramatically, so he decided to clean one GB at a time a couple of weeks apart (2 x GB's). He tried to cut corners when cleaning out the GB and a good deal of the sludge entered the FT... the following morning he had dead fish.

What would be the proper procedure? do you have to remove and wash all the media individually? can you simply fill and dump the bed a few times (untill it runs clear(ish))?

If you dont remove all of the sludge and have no/hardly any/very hardy fish, will continuing to run the setup as is fix whatever problems arise from improper washing or does the water have to be dumped?

Imagine this in a commercial scenario with a row of media beds 100ft long....

What a nightmare...

Isolate the grow bed.. so that no water can return to the sump/fish tank...

Flood the media bed to the top of the standpipe.... turn the media over.. and over...extracting all the roots and stuff....

Pull the standpipe to drain the crap... refill... repeat at least another two times.... then refill, without disturbing the bed... and dump the water... until clear... reconnect...

Or... remove the media altogether... and hose it through.. replace, flood/drain a couple of times until clear... reconnect...

Personally.. if I clean my beds/media... I then leave them fallow for a while.. before replanting...

Thanks rupert.
one thing, if commercial people ever had growbeds, especially large ones and didnt have an automated way to clean them after each harvest, well more fool them. I would also say that is operator/designer error, not the fault of growbeds.

Thanks for the instructions, i thofught it might be something like that, i dont like the idea of turning media over when using scoria though.
if a proper "dumping bed" as i have deemed them were designed (where the bottom drops away), this would stop the need to turn over the media surely? especially if worms are incorporated to eat the old roots.

What do you think?
Not that i am using/plan on using alot of beds, but i have always thought the designs people use are impractical and think they should be made to be cleaned a lot easier.

Yep.. for sure...

Why would you possibly need filtration of any kind when you have perfect filters with gravel in them that also grow plants eh?

It's so easy! Why isn't everyone doing this ?!?!?!?

I would grab some chloramX and dose the tank volume. That will rule out ammonia, nitrite. Stabilize Ph, salt to 3ppm, don't feed and observe.

Thank you for the replies! I probably do have sludge in my growbeds. They've never been flushed out.

I have a question about that though.......

In one of my growbeds, I have pepper plants. They're pretty established (again, being two years old), and they are great producers during the season.

How do you clean a grow bed that has established plants in them? I fear that if I try to pull them out, it will damage the roots and they will never recover.

So are there any tips on how to clean a grow bed which has established plants in them?

Hi tcshad. 3PPT = 3 grams per litre? Correct?

Or.. 3kg/1000L...