Why Are My Medaka Disappearing?

Why you never find a body

A medaka is a small fish, and a pond is full of things that tidy up. Shrimp, snails, and the pond's own bacteria can make a fish disappear within a day, and warm water speeds that up. So a missing fish tells you almost nothing about how it died. It only tells you the cleanup happened before you looked.

That matters, because it means "they're vanishing" and "they're dying of something specific" are usually the same problem wearing different clothes. To be clear, your cleanup crew did not kill anyone. Amano shrimp and common cleanup snails do not take healthy adult medaka, though shrimp will eat eggs and newly hatched fry they can catch. They just handle the aftermath.

Suspect one: the pre-dawn oxygen sag

If your losses are spread out, one fish every week or two through the warm months, this is my first suspect, and it's the one I learned the hard way.

Plants produce oxygen in light. At night they consume it, along with the fish and everything else alive in the water. Warm water also holds less oxygen to begin with. Put those together and the lowest oxygen of the entire day lands just before dawn, in exactly the heavily planted pond that looks healthiest in the afternoon. It rarely takes the whole pond at once. It takes the weakest fish, one at a time.

Two clues point here. First, a fish seen at the surface early in the day, working its mouth, that dies soon after. Second, a morning water temperature that's nearly as warm as the afternoon's, which means the pond never got a chance to recharge overnight.

The fixes are cheap. Keep at least a third of the surface as open water, and thin floating plants when they creep past that. Keep one gentle air source breaking the surface overnight, since the surface is where gas exchange happens, and gentle is all medaka want anyway. If you run a fan for cooling, run it at night, when evaporative cooling does its best work.

I lost every fish in one of my pots to this before I understood it. Duckweed had quietly covered the whole surface, and the pot went from thriving to empty. I wrote that story up in Can Floating Plants Kill Fish?

Suspect two: predators you can't see

Dragonfly nymphs and backswimmers both take small fish, and both arrive without an invitation. Nymphs often ride in as eggs on new plants and then hunt underwater for months. If your pond is inside a screened enclosure, you can mostly cross flying adults off the list, but check new plants before they go in.

Birds, raccoons, and cats announce themselves less politely. They tend to take several fish at once and leave the pond disturbed, so slow steady losses usually are not them.

Suspect three: they jumped

Medaka jump, especially when startled, when water quality dips, or when a male is chasing. A jumped fish lands outside the pond, dries out fast, and is easy to miss or easy for something else to find first. If your water level sits close to the rim, that's worth fixing. More in Do Medaka Jump?

Suspect four: numbers you haven't actually seen

"The water is fine" needs to mean readings, not appearance. Ammonia, nitrite, pH, and KH, from an actual test. Chronic low-grade ammonia irritates gills and weakens fish slowly, which looks exactly like fish quietly vanishing over weeks. If you catch a struggling fish, move it to a container and look closely at the gills and body before the cleanup crew gets a vote. My sick fish guide covers what to look for.

The longer tail

If the big four come up clean, the list keeps going, and some of these are hard to prove. Plain old age, since a pond stocked all at once declines all at once a couple of years later. Chronic internal disease that shows nothing on the outside. Low KH letting the pH swing hard in a heavily planted pond. Top-off water that carries chlorine or chloramine. Neighborhood mosquito spraying or lawn treatments drifting onto the water, which is worth thinking about on decks and patios. Bullying in an overstocked or male-heavy pond. None of these is the place to start, but a stubborn case is usually hiding in this paragraph somewhere.

The order I'd check things

1. Temperature at dawn. If the morning is nearly as hot as the afternoon, oxygen moves to the top of the list.

2. Oxygen at first light, if you can test it. Compare against evening.

3. Surface coverage. More than about two-thirds covered by floaters is too much.

4. Real water readings, not a glance.

5. New plants and pond edges for hitchhikers.

6. Water level and jumping room.

Most quiet-loss ponds I hear about come down to the first three.