You dreamed of a peaceful koi pond: sparkling water, colorful fish gliding like living jewels, gentle waterfalls whispering in the background. And then reality showed up with a bucket of chaos: mysterious water loss, green soup algae, and koi acting like drama queens.
Take a breath. Every koi keeper, from beginner to master, has faced pond problems. The trick is learning to read your pond like a story rather than a disaster. In this long-form guide, we’ll walk through how to troubleshoot the three big headaches:
- Leaks – where is the water going?!
- Algae – green water, string algae, and the “pea soup” apocalypse
- Fish loss – sudden deaths, gasping, or “something’s just off”
Think of this as your pond’s emergency manual — but written by a friend who also laughs at how dramatic koi can be.
Part 1: Leaks – When Your Pond Starts Disappearing
Few things are more alarming than looking at your pond and thinking, “Was the water level… there yesterday?” But before you start pricing new liners or calling in an exorcist, let’s slow down and troubleshoot.
Step 1: Is It Really a Leak? (Evaporation vs. Actual Problem)
First question: are you sure it’s a leak, and not just evaporation or splash-out?
Normal evaporation and splash can cause:
- Loss of 0.25–1 inch per day in hot, dry, or windy weather
- More loss if you have big waterfalls or streams
- Faster drop in smaller, shallow ponds
To test this, try the bucket test:
- Fill a bucket with pond water and place it next to the pond.
- Mark the water level on both the bucket and the pond (use tape or a pencil mark on a rock).
- Wait 24–48 hours without adding water.
- Compare the drop in the bucket vs. the pond.
If both dropped about the same, it’s likely evaporation. If the pond dropped significantly more, you probably have a leak to hunt down.
Step 2: Narrow Down the Leak Zone
Leaks usually fall into a few categories:
- Pond liner (holes, punctures, folds, edges)
- Plumbing (pipes, fittings, bottom drains, filter lines)
- Waterfalls and streams (the #1 culprit more often than people think)
A quick detective trick:
- Turn off the pump and filtration system.
- Let the pond sit for 24 hours.
If the water level stops dropping once the pump is off, the leak is likely in:
- Waterfalls or streams (water escaping over liner edges)
- Plumbing between pond and filter
If the water level continues to drop even with the pump off, the leak is probably:
- In the main pond basin itself (liner, bottom drain, skimmer)
Step 3: Use the “Waterline Clue”
As the water drops, pay attention: it will usually stop at the level of the leak. That “resting waterline” is like a big neon sign saying, “The problem is somewhere right around here.”
Once it stops dropping:
- Inspect that exact height all around the pond edge.
- Look for folds, creases, animal damage, roots, or low spots where water might escape.
- Check around skimmer openings and penetrating fittings.
Common Leak Spots (and Fix Ideas)
1. Waterfalls & Streams
These are drama factories.
- Liner not extended high enough at the sides
- Rocks redirecting water over the edge
- Shifted stones after freeze-thaw or kids/dogs/clumsy humans
Fix: Reposition rocks, raise liner edges, add “splash dams” or small barriers to keep water inside the stream channel.
2. Liner Punctures
Caused by rocks, roots, critters, or tools.
- Feel for soft spots where liner isn’t supported by soil
- Inspect visible areas for tiny punctures or tears
Fix: Use a proper pond liner patch kit (EPDM-compatible if that’s your liner). Dry, clean, and patch per instructions.
3. Skimmer and Bottom Drain Areas
Anywhere the liner is cut and clamped is a potential offender.
- Check screws, faceplates, and gaskets
- Look for cracks in plastic housing
Fix: Tighten loose screws (evenly!), replace gaskets, reseal with pond-safe sealant if necessary.
4. Plumbing Leaks
Pressurized lines can drip or spray where you can’t easily see.
- Inspect all above-ground connections
- Listen for hissing or spraying
- Check for damp soil, mushy spots, or mysterious wet patches along pipe routes
Fix: Replace cracked fittings, use proper PVC primer and cement, and avoid over-tightening threaded fittings (which can crack).
Remember: a methodical approach beats panic every time. The pond isn’t out to get you — it’s just telling you something is out of balance.
Part 2: Algae – From Green Soup to Stringy Mess
Algae is the annoying cousin that shows up uninvited, eats all the snacks, and refuses to leave. But here’s the truth: some algae is normal. The goal isn’t a sterile, algae-free pond — it’s balance.
The Three Big Types of Algae Trouble
1. Green Water (Pea Soup)
Suspended microscopic algae. You can’t see your fish. Your pond looks like blended spinach.
2. String Algae (Filamentous Algae)
Long, hair-like strands that drape over rocks, waterfalls, and surfaces. Slimy and deeply rude.
3. Slippery Algae Film
Green or brown coating on liner and rocks. This one is mostly good: it’s part of a healthy pond ecosystem, so don’t obsess over it.
Why Algae Blooms Happen
Algae is basically a plant with no chill. Give it:
- Sunlight
- Nutrients (fish waste, uneaten food, decaying leaves)
- Warm water
…and it will throw a rave.
Step 1: Check Your Water Quality
Any time algae goes wild, grab your test kit. Check:
- Ammonia
- Nitrite
- Nitrate
- pH
High nitrates (and sometimes phosphates, if you test for them) often fuel algae. If nitrates are climbing, your pond is basically a salad bar for green stuff.
Step 2: Attack the Root Causes, Not Just the Symptoms
Reduce Nutrients
- Avoid overfeeding — koi will always act hungry. They are professional liars.
- Vacuum or net out leaves and sludge.
- Rinse filter media in pond water (not tap) to keep bio bacteria alive.
- Do regular partial water changes to dilute nutrient buildup.
Improve Filtration and Circulation
- Make sure your biofiltration is adequate for your fish load.
- Increase flow through filters if needed.
- Add aeration – oxygen supports beneficial bacteria that outcompete algae.
Add Plants to Compete With Algae
- Floating plants (water hyacinth, water lettuce where legal)
- Marginals and bog filters
- Water lilies for shade and nutrient uptake
Plants steal the nutrients algae wants. Rude to algae; great for koi.
Green Water: Specific Solutions
If your pond is full-on pea soup, consider:
- UV Sterilizer: A properly sized UV unit is the ultimate green-water buster. It kills suspended algae as water passes through.
- Shade: Add shade sails, more lilies, or plantings to reduce direct sun.
- Patience: A new pond often experiences green water while the biofilter matures. Don’t chase it with chemicals if the fish are fine.
String Algae: Specific Solutions
String algae is stubborn but beatable.
- Manual removal: Use a toilet brush, stick, or gloved hands to twirl it out like green spaghetti.
- Flow control: It loves slow-moving areas. Increase flow where possible.
- Reduce excess light and nutrients: Same playbook as above.
- Biological time: In many ponds, string algae surges, then fades as plants and biofilms stabilize.
Be careful with algaecides. Many can cause oxygen crashes when algae dies suddenly, which can seriously harm or kill koi. If you ever use them, aerate like crazy and follow directions to the letter — but ideally, rely on long-term natural control instead of “chemical carpet bombs.”
Part 3: Fish Loss – When Your Koi Are in Trouble
Few things gut a koi keeper like walking out to the pond and finding a fish in distress — or worse. Before you blame a mysterious koi curse, let’s walk through a structured troubleshooting approach.
First: Take a Deep Breath and Gather Clues
When something goes wrong, your job is half detective, half paramedic. Ask yourself:
- Did this happen suddenly or gradually?
- Are all fish affected, or just a few?
- Any recent changes? (new fish, new food, new equipment, storms, chemicals, construction nearby, etc.)
- What behaviors are you seeing? (gasping, flashing, clamped fins, isolation, jumping, floating, sinking)
Step 1: Test the Water — Always
In pond keeping, water quality issues cause more deaths than disease or predators.
Immediately test:
- Ammonia
- Nitrite
- Nitrate
- pH (and if possible, KH)
- Temperature
If Ammonia or Nitrite Are Above 0
- Do an immediate partial water change (25–50%) with dechlorinated water.
- Add extra aeration.
- Apply ammonia binder if needed (pond-safe).
- Stop or reduce feeding until levels are safe again.
- Check if your filter is cycled, overloaded, or recently disturbed/cleaned too aggressively.
If pH Is Swinging or Too Extreme
- Big pH swings (morning vs. evening) can stress or kill koi.
- Stabilize KH (carbonate hardness) to buffer pH by using appropriate products or crushed coral, baking soda (carefully, in controlled amounts), etc.
Signs of low oxygen:
- Fish gasping at the surface or hanging near waterfalls
- Struggling during hot weather or at night
Fix:
- Add air stones or more aeration.
- Increase surface agitation.
- Avoid overcrowding and heavy feeding during heat waves.
Step 2: Rule Out Toxins and Contamination
Sometimes the pond is fine… until something nasty sneaks in.
Possible culprits:
- Lawn chemicals or fertilizer runoff
- Paint, solvents, or cleaners dumped nearby
- New untreated wood leaching toxins
- Concrete work altering pH
- Children “helping” by adding soap or random substances
If you suspect toxins:
- Do multiple partial water changes.
- Add activated carbon in a filter bag to absorb contaminants.
- Boost aeration.
Step 3: Look for Parasites and Disease
Once water quality and toxins are ruled out (or corrected), then consider parasites or infections.
Common signs:
- Flashing (rubbing or scraping against surfaces)
- Clamped fins
- Mucus or slime coat excess
- White spots (ich)
- Red streaks in fins or sores on the body
- Isolation (fish hiding alone)
Ideally, you’d confirm with a skin/gill scrape under a microscope, but not every hobbyist has that setup.
General best practices:
- Quarantine new fish before adding them to the main pond.
- Avoid “mystery” treatments without a good reason — some medications can stress koi and biofilters.
- Consult experienced koi keepers or a fish vet if possible.
Step 4: Consider Stress and Overcrowding
Even if water tests look okay, chronic stress wears down koi over time.
Stress factors:
- Too many fish for the pond size or filtration
- Constant predator visits (herons, raccoons, cats)
- Frequent netting, chasing, or moving fish
- Lack of hiding spots or shade
- Sudden temperature swings
Reduce stocking density, improve shelter, and keep the pond as calm and predictable as possible. Koi may be bold, but they really appreciate stability and quiet.
Step 5: Predators and Physical Injury
If you’re finding koi with injuries, missing fish, or odd behavior at dawn, predators might be involved.
- Look for footprints around the pond.
- Check for scales or partial bodies near the edge.
- Notice if koi are suddenly skittish or hiding constantly.
Consider adding:
- Deeper water (2–3 feet minimum, more for heron-prone areas)
- Netting or fishing line barriers
- Hiding caves and tunnels
- Motion-activated lights or sprinklers
Putting It All Together: Your Pond Troubleshooting Mindset
When your pond misbehaves, it’s easy to feel frustrated or overwhelmed. But remember:
- Leaks are solved by methodical isolation: pump on vs. off, watching the waterline, inspecting edges and fittings.
- Algae is a symptom of imbalance, not a villain you can permanently murder with a one-time product. Think nutrients, light, filtration, and ecosystem health.
- Fish loss almost always circles back to water quality, oxygen, toxins, stress, or disease — and water testing is your first and best tool.
The more time you spend watching your pond, the more fluent you become in its “language.” You’ll start noticing subtle changes long before they turn into emergencies — and that’s when koi keeping turns from stressful to deeply satisfying.
Your pond will have problems; that’s normal. But with a calm, curious, step-by-step approach, you can fix them, learn from them, and come out the other side with a healthier pond… and even more respect for those gorgeous, dramatic fish that started this whole adventure.