Why are all my pond fish dead after heavy rain?

There is probably nothing more disheartening for a pond owner than to find prized and nurtured koi, goldfish, minnow and other pond fish dead in the water. This phenomenon is often associated with high or heavy rainfall and cloudy periods.

It’s not common to see pond fish dead after heavy rain but it also happens.

It is often sudden and always unexpected, and can affect even a properly maintained pond with previously thriving fish. 

Rain appears to be harmless to ponds, but heavy rainfall is not to be underestimated and can be an overlooked aspect of pond care with devastating effects.

In this article, we will help you understand how strong rains and storms can affect your pond fish and the action you need to take to protect a re-stocked pond in the future.

Key effects of heavy rains on ponds 

When you create a pond you are establishing a contained ecosystem, with interdependence between your fish, plants and other aquatic organisms, including microorganisms.

As an owner, you work to maintain this environment, and its parameters, so that the living things within the pond can thrive and replenish themselves. 

Ideally, you would want to mitigate the effects of sudden changes but heavy rain, especially overnight leaves no time for that. 

A deluge of rain will impact your pond ecosystem in the following 4 ways. 


Ponds typically have some degree of stratification or layering, where warmer, better-oxygenated water tends to be near the surface of the pond and colder, oxygen-poor water at the bottom. 

Fish naturally congregate where their vital supply of oxygen is most abundant in the pond.

A deluge, with rainfall of more than two inches, changes all that. The volume of water can cause sudden mixing or ‘turnover’ of the pond with the oxygen-depleted pond water from the bottom of the pond being displaced and mixed in with the better-oxygenated portion.

This leads to a net decrease in oxygen concentration across the pond which can cut off the oxygen supply to the fish and kill them. This phenomenon is most common overnight, where oxygen levels in ponds tend to be at their lowest and a sudden drop in water temperature can also stun fish and hasten death.


Rainy, cloudy weather can also produce large shifts in the population of phytoplankton, a key oxygenator in ponds. Clear skies and sunny days see these microorganisms hard at work using sunlight for photosynthesis and releasing oxygen into your pond water as a by-product. 

Stormy and cloudy weather cuts short this process and switches them to becoming net consumers of oxygen which can rapidly deplete the pond’s oxygen levels, especially if their numbers are expanded.

This leaves pond fish short of oxygen, with larger fish succumbing first. 

3.Water chemistry shifts

Unless cultivating a wildlife pond with no fish, optimal water chemistry will be essential for the viability of your pond. Fish especially need water parameters such as:

  • pH
  • Specific gravity
  • Water hardness
  • Nitrates and nitrites
  • Salinity

to be maintained within strict limits. For fish such as koi, fluctuations in water chemistry can be just as harmful as frank derangement, so pond care will involve testing and adjusting water levels as needed.

Sudden, large volume rainfall can drastically shift the water chemistry in a pond. Rainwater absorbs atmospheric gasses, chemicals, and pollutants on its way to your pond and in particular, has a tendency to be acidic.

This will not only acidify a pond but also potentially introduce toxins such as lead, zinc, and cadmium that can poison your fish.

4.Surface runoff

In prolonged rainy weather, your pond can become the end of the line for rainwater that has washed down a variety of surfaces and drained through the soil. Rainwater that drains into a pond may have come into contact with:

  • Fertilizers (a particular problem if you are in the proximity of a working farm)
  • Metals from roofing or gutters
  • Pesticides
  • Weedkiller

All these substances can be washed into your pond where they can accumulate, poison and kill your pond life.

pond fish dead after heavy rain

How can I prevent a rain-induced fish kill in the future?

Taking some simple steps to prevent or at least limit the effect of heavy rain can be life-saving for your pond.

Try implementing some or all of these strategies:

  • Adding or increasing existing aeration. You can reduce the risk of rain-induced asphyxiation of your fish by ensuring that your water is properly circulated by an effective pond pump waterfall or fountain. Ensure that your pond pump is rated for the size of your pond.

See a suitable range of pond aerators here on Amazon ↗️

  • Check water chemistry after rains and take action quickly. As soon as you have had heavy rain, it is well worth testing your pond water to ensure that your fish are not being stressed. Correct derangements quickly with appropriate additives, removing the fish if necessary. 

  • Take care with vegetation. Aquatic plants can be both friend and foe due to their simultaneous production and demand for oxygen. Excessive growth and spread of your pond plants can rapidly deplete oxygen if there is an acute challenge to supply as in the event of heavy rain.

  • Raise the level of your pond to prevent surface runoff. Raising the rim of your pond will prevent leaching of fertilizers and pesticides into your pond water.  

  • Drainage will also protect your pond from the effects of runoff and can range from aerating lawned areas to the installation of shelved drainage within the pond or surrounding the pond to divert water away from it. 

  • Mechanical and biological filtration can also assist in mitigating the effects of fertilizers, clippings and rotting vegetation that can be washed into your pond to ensure that your water remains as clear as possible.
white middle aged woman cleans fish pond from slime and water plants. Spring and summer seasonal pond care work

In conclusion: pond fish dead after heavy rain

Heavy rain can appear innocuous, but be devastating for your fish. The simple steps outlined above will tackle the key ways in which wet weather harms your fish.

Being prepared for the effects of severe weather on your pond will not only keep your prized fish safe but contribute to the overall health and resilience of your pond.