Pondology 101: What To Do When It Floods
- Jared Engelbert

- Jun 27
- 9 min read
Updated: Jun 28

The world of pond management comes with many natural phenomena that can ameliorate or exacerbate pond issues.
Runoff from rain is essential for most ponds with an earthen dam (unless you’re fortunate enough to have a perennial spring filling your pond). In most cases, Luke Bryan is correct, “Rain is a good thing”! Rain is great in moderation. When you get a half inch to an inch of rain, the water usually trickles and flows down through grass and vegetation and eventually into your pond. If your watershed is mostly made up of grasslands, the water and debris is filtered out before it reaches your pond (most of it). This is a nice healthy addition of clean and fresh water to your pond.
If your area was in a drought, your pond might not even see any of that water because the ground soaked it up like a sponge. In this case, you’ll probably need a gulley washer to see some inflow. This was the case for my area throughout most of Kansas until this spring. The ground was extremely dry and soaked up the first few rains. But the rain kept coming and coming. The ground was saturated, and any rainfall practically flowed straight to the nearest creek, ditch, or pond. We’ve had a couple “toad croakers” here in Kansas this year, which has filled everyone’s ponds… but the issues swept in with the rain.
What happens to ponds during floods?
Nutrients flow in (debris, organic matter, fertilizer, nutrient-laden soil, etc.)
Stratified ponds “turnover”
Water levels rise quickly
Outlet pipes get clogged
Emergency spillways erode
In worst case scenarios, dams breach and/or break
Possibly the worst thing that can happen, is a fish kill. If your dam breaks, you have bigger fish to fry. Let’s say your dam held up through the flood, the skies have cleared, and you’re left with a plumb full pond.
This is what you’ll see for the next 3 days or so.
First, the water will be very murky with the suspended soil and clay particulates that swept into your pond from the flood. This shades the water column and blocks sunlight and inhibits oxygen-producing photosynthesis from occurring.
All of the debris and organic matter that flowed into your pond begins to anaerobically decompose, which consumes more oxygen. The water will begin to look stagnant with a nasty poopish-brown tint to it. Now remember that your pond “turned over”, so that means a bunch of nutrient-laden muck was resuspended. Methane, hydrogen sulfide, and sulfur were mixed throughout the pond too, which are toxic to fish at high levels. It will at least stress them out and make them more vulnerable to other stressors. Also, when ponds are stratified, there isn’t any oxygen below the thermocline. Most ponds that are deeper than 8 feet will set up a thermocline between 6 and 8 feet deep. I won’t go too far into detail about pond limnology, but essentially it is “dead” water with a buildup of toxic gases. The combination of no oxygen and toxic gases getting mixed into the rest of the pond during a turnover event is bad news for the fish. This alone can cause a fish kill in some cases.
The first 2 stressors can cause partial fish kills, and in severe cases, complete fish kills. The last stressor to arise from a flood event usually puts the final nail in the coffin. The sudden influx of nutrients creates an extremely hypereutrophic system. A couple days after the flood, the organic matter, debris, flooded terrestrial vegetation, and resuspended bottom sediments have been decomposed. The nutrients released from all of the aforementioned byproducts are now bioavailable. This causes a sudden burst or “bloom” of planktonic algae, or cyanobacteria. Most likely, the initial bloom will be composed of cyanobacteria (blue-green algae; BGA), because it has the ability to form gas vesicles and float to the top of the water column, whereas green algae does not have this adaptation. The BGA becomes very dense and shades the entire water column, outcompeting everything else for sunlight and resources. It replicates exponentially during the day and becomes so thick that it looks like pea soup! If you tested the dissolved oxygen in the middle of the day it would be supersaturated, which means the dissolved oxygen levels are very high from photosynthesis. You would think this is a good thing, right? Well, BGA are insidious in a manner that they can produce their own toxins. These cyanotoxins can cause fish kills, and they can also kill terrestrial animals that decide to take a swim or drink from the pond.

A very dense cyanobacteria or Blue-green Algae bloom a few days after a major flood event. I was going to tie this one into the 3rd stressor, but I decided it needed its own section. So, if the fish survived the first 3 stressors, you have some very resilient fish! The last stressor is the nighttime DO crash from the extremely high biological oxygen demand (BOD). In other words, the oxygen-producing BGA that exponentially grew during the day, respires throughout the night. The high rate of respiration leaves the water with very little DO for the fish. Given all of the previous stressors, the fish are already very vulnerable, and this is almost always the final straw.
You can’t prevent Mother Nature from happening. When she decides it’s going to flood, it’s going to flood. You might ask; “What’s the point of spending my time and money on a pond if it’s inevitably going to flood and spur the chain of events you described and potentially kill all of my fish?”. The answer to that question is why you’re reading this. You’ve most likely gone through this situation before, or you are desperate for some quick answers because this is happening to your pond right now. Fortunately, there are a few proactive and reactive critical management strategies that you can implement to avoid a complete fish kill.
Proactive Pond Management Strategies To Avoid A Flash Flood Fish Kill Event
Pond Design & Construction- If you’re looking to build a new pond and wanting to avoid chronic turnover-related fish kill events, here’s what you need to think about when designing your new pond.
Surface area to volume ratio (SA/V) is the determining factor of a pond’s susceptibility to environmental factors, such as wind and solar radiation. Ponds with a high SA/V ratio are shallow compared to its size. Ponds with a low SA/V ratio are relatively deep compared to its size.
In ponds with a high SA/V ratio (shallow), the wind is constantly mixing the water column. Sunlight can penetrate a large percentage of the water column, which means it warms most of the pond relatively evenly. Photosynthesis occurs in most of the water column as well, consequently adding dissolved oxygen at most depths. Additionally, even if it is a murkier pond- which is the case with most shallow ponds due to wave action disturbing the bottom sediment- the oxygen produced at the top of the water will be mixed throughout all depths due to the wind.
Contrastingly, ponds with a low SA/V ratio (deep) have a tendency to stratify during the summer. This means that a thermocline sets up due to the lack of mixing between the epilimnion (top warm layer) and the hypolimnion (bottom cool layer). The thermocline, also known as the metalimnion, is the middle layer of a pond where there is a rapid decrease in temperature with depth. There is little to no mixing between the epilimnion and hypolimnion, and the thermocline acts as a “cap” between the two layers. In the hypolimnion there is almost no dissolved oxygen because sunlight can’t penetrate to its depths and decomposition of organic matter “sucks out” all of the dissolved oxygen, creating an anoxic environment (dead zone). Additionally, the byproducts of anaerobic bacterial decomposition build up in the hypolimnion (hydrogen sulfide, methane, sulfur).

All ponds turnover naturally in most areas throughout the United States. Once in the spring and once in the fall (dimictic). The severity of these turnover events is directly related to the SA/V ratio. The most dangerous turnover events happen after the thermocline has set up in the late spring or early summer. Thus, a turnover event is likely to occur after a heavy rainfall event. Because the rainwater is cooler and denser than the water in the epilimnion, it causes that water to be “pushed” downward into the hypolimnion. Consequently, this mixes all of the toxic gases and oxygen-poor water throughout the entire water column. This can lead to a fish kill or the first and second stressors we talked about earlier.
Going back to pond design, it is wise to build a pond that has at least 8 to 12 feet of depth to account for evaporation and drought. Deeper ponds also have a larger volume, which helps dilute toxins, buffer temperature fluctuations, reduce vegetation and algae growth, and aids in nutrient cycling. A good rule of thumb is to have 50 percent of your pond reach a depth of at least 8 feet.
How can you prevent a harmful turnover event?
The silver bullet is a properly sized bottom-diffused aeration system. These systems are made up of a compressor or multiple compressors that pump air through weighted tubing and out of diffusers placed on the bottom of your pond. The bubbles that come out of the diffusers create an uplifting motion. The upward motion of the water displaces the water at the top, which creates a constant churning of the water column. This eliminates the thermocline and consequences of stratification. A constant churning and mixing of the water column allows toxic gases to “gas-off”. Oxygen produced at the top mixes to the deeper water, which supports beneficial aerobic bacteria to thrive. The presence of oxygen in deeper water helps bind up phosphorus with other molecules making it unavailable to biological processes (plants and algae).
"An aeration system is essentially an insurance policy for your fishery."
It is VERY important to properly size your aeration system, because if it is undersized, it can make things worse. An undersized system won’t thoroughly mix the entire water column, which won’t eliminate stratification. A short explanation- since an undersized system doesn’t eliminate stratification, toxic gases still build up in the hypolimnion and are released and mixed into the epilimnion via air bubbles from the diffusers. An undersized system is literally a “pumphouse” for the toxic gases. This leads to a chronic and downward spiral of your water quality and fish health. Not ideal. I explain in great detail on how to properly size your aeration system in “The Ultimate Pond Management Playbook”, among other in-depth explanations and pond management strategies.
Surface aeration won’t necessarily prevent a turnover, but it will give refuge to the fish during stressors. The key takeaway is: a well aerated pond with high dissolved oxygen levels will significantly reduce the chance of a harmful turnover event.
The 2 main proactive measures were pond design and proper sized aeration. Let’s take a look at what to do in a state of reaction to a flood event and how to avoid a fish kill.
Reactive Pond Management Strategies To Avoid A Flash Flood Fish Kill Event
Your pond just got flooded and you notice that the water is looking nasty and there’s a blue-green algae bloom in full bloom. What do you do?
The water needs as much agitation as possible. Assuming you don’t have a surface aerator handy, go get every water pump you can get your hands on and spread them around the pond. Point the outlet hose up in the air like a fountain. Get your boat out on the pond with the outboard trimmed up so it’s throwing water in the air and spin some kitties! I’ve even left the boat on the trailer and trimmed the outboard so that its shooting water into the air. Call your buddies and have them bring their boats too! Just do what you gotta do to agitate and throw as much volume of water into the air as possible. By doing this, you’re increasing the dissolved oxygen in the epilimnion and helping your fish survive.
Agitating the water is an immediate necessity if you see your fish piping at the surface or if you are already seeing dead fish. Once you have the agitation in place, you’ll want to address the active blue-green algae bloom. The best control method in this situation is using a peroxide-based algaecide. The algaecide will kill the blue-green algae and in the process of the chemical reaction with water, it actually releases oxygen. This simultaneously kills the blue-green algae and increases the dissolved oxygen levels. Keep in mind that you don’t want to kill too much at once, because the decomposition process can suck oxygen out of the water too. I play the wind and treat the downwind areas of the pond to avoid collateral damage. If it is really windy, all of the blue-green algae will be concentrated on the downwind side anyways.
Now you know how to proactively set your pond up to avoid harmful turnover events, and how to reactively save your fish in an emergency situation.
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