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How to Keep Pond Water Clear – The Ultimate Guide

    Splash Supply Company Ecosystem PondAlgae, muck and murky water.

    They’re the most common complaints we hear from pond owners. Luckily, they’re also the easiest to solve and prevent.

    Before we talk about how to clear up your water, though, let’s clear up some misconceptions about pond muck and algae.

    First, most algae – including green-water algae and string algae – pose no risk to your fish. The only reason they’re “problems” at all is most people don’t like the way they look. If you don’t mind green-tinted water or fuzzy rocks, you can stop reading here and go on enjoying your pond.

    Second, all ponds will always have a little bit of algae and sludge. Your pond is a living ecosystem, not a swimming pool. Agonizing over every bit of green in your pond doesn’t make for a relaxing oasis.

    That all being said, keeping your water crystal-clear and algae in-check isn’t hard to do. And you can do it without using potentially dangerous algaecides.

    IN THIS GUIDE: How to Keep Pond Water Clear

    Designing Your Pond for Clear Water

    Clear water starts with good filtration. Period. No amount of product you add to your pond will make up for poor filtration.

    So what is filtration?

    Filtration comes in two forms: physical and biological.

    • A physical filter, commonly known as a skimmer, removes 80 to 90 percent of the leaves, fish waste and other debris that ends up in your pond.
    • A biological filter, also called a biofilter or Biofalls, has lots of nooks and crannies where beneficial bacteria colonize. These bacteria help keep your water clear. The water runs up through the biofilter then out through your waterfall.

    These filters are the cornerstones of Ecosystem Pond design. An Ecosystem Pond is simply a water feature that uses some clever man-made tricks to replicate processes that happen in nature.

    In our 30 years of experience building ponds, we’ve found that the Ecosystem Pond model is the best for keeping water crystal-clear. If you haven’t built your pond yet – or you’re looking to upgrade – consider using the Ecosystem Pond as your template.

    What Kind of Algae is in My Pond?

    The first step to clearing up your pond water is figuring out what’s in it. If the problem is something green, you probably have algae.

    And the first step to fixing algae problems is understanding what kind of algae you have.

    Most pond algae falls into one of two categories: string algae or single-cell algae. String algae, also known as filamentous algae, is the gunky stuff that clings to your rocks. Single-cell algae is the microscopic stuff that turns your water green.

    Knowing which kind of algae you have is important because each type requires different treatment. Luckily, telling the two apart is simple. If your water is clear aside from stringy clumps that you can pick up with your hands, you have string algae. If your water is pea-soup green, you have single-cell algae.

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    How to Fix Green Pond Water

    All you need to do to prevent and treat green water in your pond is starve the single-cell algae that causes it. You can do that by making sure your water has plenty of beneficial bacteria.

    Here’s how it works: Single-cell algae thrive on nitrites, a byproduct of ammonia breaking down in the pond. Beneficial bacteria eat these same nitrites. When you add beneficial bacteria, you remove the algae’s food and starve it – giving you clear water.

    You can take two simple steps to ensure your pond has plenty of bacteria:

    1. Add regular doses of beneficial bacteria.
    2. Make sure your pond as adequate filtration.

    How to Add Bacteria to Your Pond

    Beneficial bacteria pump bottleBeneficial bacteria naturally grow on your rocks and in your biofilter, but you need to give them a boost with regular doses of extra bacteria.

    You have two options for how to do this: by adding a weekly dose of bacteria yourself from a pump bottle, or by installing an autodoser that dispenses tiny doses of bacteria into your pond every day.

    Both methods will come with instructions to help you understand how much and, in the case of autodosers, what type of product to add to your pond.

    • Adding Bacteria using a Pump Bottle:
      • We sell two types of beneficial bacteria products at Splash for green water. One is labeled “Beneficial Bacteria,” which, as the name implies, is just bacteria. The other is labeled “Maintain”: bacteria mixed with phosphate binder, flocculant and pond detoxifier.
      • Regardless of which bacteria product you choose, you need to add the treatment to your pond at least once a week, even after the water has cleared up (and, if possible, before the water turns green, as a preventative measure.)
      • Both of these products are completely safe for fish, so you can up the dosage to two or three times a week if you feel your pond needs it.
    • Adding Bacteria with an Autodoser:
      • If you have an autodoser, start your fight against green water by using the “Maintain for Ponds” bag if you aren’t using it already.
      • If the water still isn’t clear after a few weeks, switch to “Clear for Ponds” until the green is gone, then switch back to the “Maintain” bag to prevent algae from coming back.
      • The “Clear for Ponds” bag contains a small amount of algaecide, so follow the dosing instructions carefully to avoid harming fish.

    How Long Does Bacteria Take to Clear Up Green Water?

    How long any type of beneficial bacteria takes to make your water clear depends on a number of factors, including the age of the pond, the time of year and the quality of your filtration system.

    Newly installed and newly cleaned ponds will take longer to clear up than established ones because the beneficial bacteria has not yet had a chance to settle in. Ponds also often go through a green phase in the spring as bacteria kicks back into gear after winter.

    You can generally expect to wait a few weeks before you start seeing results from any bacteria product. But if you keep up with regular treatments, your water will stay clear from then on IF – and, again, this is important – your pond has adequate filtration and you keep up with preventative doses of bacteria. If you stop adding bacteria, your water will turn green again.

    Checking Your Filtration

    If you’ve been diligently adding beneficial bacteria to your pond for several weeks and still find yourself staring into a green murky mess, you need to upgrade your pond’s filtration system.

    Ponds have the clearest water when they have a biofilter and skimmer running 24/7. The skimmer removes physical debris from the pond – i.e. dead leaves and fallen twigs – while the biofilter has lots of nooks and crannies where beneficial bacteria can reproduce before circulating out to the pond through your waterfall.

    If your pond lacks either of these filters, or your filters are too small, you’ll have a much harder time keeping your water clear.

    Inadequate filtration will cause even more headaches if you have lots of fish in your pond. Only add as many fish as your filtration can handle.

    Finally, all the filtration in the world won’t do you any good if you’re constantly wiping out your pond’s beneficial bacteria. You can clean your skimmer as much as you’d like – most people choose to do so about once a week – but only clean your biofilter once a year, preferably in the spring before the bacteria has established itself for the season.

    Does Algaecide Work to Clear Green Water?

    Some pond owners like to use algaecides to clear up green water. These products kill algae quickly but can cause more trouble than their worth.

    First, you need to follow dosing instructions very carefully if you decide to try algaecide in your pond. Adding even just a little too much will cause oxygen levels in your water to plummet and can potentially kill your fish. Always run an aerator in your pond while using algaecide.

    Second, all the algae that the algaecide kills will sink to the bottom of your pond, where it decomposes and becomes food for new algae. All the while, you still haven’t done anything to treat the problem that caused green water in the first place: excess nutrients in the pond. Using algaecide without supplementing with beneficial bacteria will send you into an endless cycle of buying bigger and bigger containers of algaecide.

    Do UV Clarifiers Work to Clear Green Water?

    Here’s the truth about UV clarifiers: You don’t need them. We have never in our 30-year history had to install a UV to clear up green water.

    UV clarifiers kill single-cell algae by running your pond water past a UV bulb that damages the algae’s cells. UVs are safe for fish and often effective against green water, but if your pond has the right filtration and enough beneficial bacteria, you shouldn’t need to bother with them.

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    How to Prevent and Treat String Algae in Your Pond

    String algae is the slimy stuff that clings to your rocks – and it’s a normal part of a pond ecosystem.

    Almost every pond has some string algae. It won’t hurt your fish or plants when present in moderate amounts. If you don’t mind the way it looks, you can usually leave it alone.

    But what if string algae takes over – or you simply get tired of looking at it, or want to prevent it from growing in the first place?


    Floating Plant Island with Star GrassThe easiest way to keep string algae at bay is to add more plants to your pond. String algae eat nitrates – a nutrient that naturally comes into the pond when beneficial bacteria do their work.

    Plants also eat nitrates. Each type of plant you add to your pond will take in a different kind of nitrate – i.e. a red leaf will absorb one type, a green leaf another. The more and wider variety of plants you add to your pond, the fewer nutrients are left to feed string algae.

    Contact Algaecides

    Plants will always give you the best defense against string algae. But if you already have a huge variety of plants in your pond, and you’re still not happy with the amount of string algae on your rocks and waterfalls, you can buy a few products to give your pond that final polish.

    The first product we recommend for getting rid of string algae is a powder like S.A.B. or EcoBlast. Simply sprinkle the powder directly on the algae per the directions on the container. Remember to remove any dead algae from your pond as soon as possible, before it becomes food for new algae.

    Barley Straw Extract

    Barley Straw ExtractThe second product we recommend for string algae is barley straw extract.

    Barley straw extract won’t kill string algae that’s already in your pond, but some pond owners find it helps prevent new string algae from growing. You can buy barley straw in a few forms – bales, pellets and extracts – but our customers typically report the most success with liquid extract.

    Barley straw doesn’t work for everyone, but it’s worth trying if you want an easy, natural way to prevent string algae.


    Some pond owners like to install an ionizer for constant string algae deterrence. These devices – marketed under names like the IonGen – release metal ions into the water through a probe, creating conditions that string algae don’t like.

    Ionizers can be a powerful tool for creating a pristine water feature, but they carry a hefty price tag: $300 or more for the unit, plus upward of $100 for probes that need replaced every one to three years.

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    Other Water Clarity Issues

    Algae causes is the most common water clarity issue that pond owners encounter. Sometimes, though, other factors can also make water a little messier or murkier than you might want.

    Brown Tinted Water

    Certain kinds of trees, mulch and other organic debris can give your otherwise clear water a brown tint. The tint alone won’t hurt your pond, but, if you don’t like the way it looks, you can use activated pond carbon to help clear things up.

    The science behind carbon is a little complicated, but it essentially grabs the brown-color tannins out of the water. It also takes out stuff like chloramines and certain odor-causing compounds.

    Murky Water

    Is your water brown and murky? If you’ve already tried treating for algae (which is typically more green), you might just have a bunch of suspended debris in the pond.

    Lots of things can stir up muck in your pond. Some common causes include clean-outs, heavy rain, mating fish and newly-added plants.

    You can clear up murky water by adding a pond flocculant like Rapid Clear. You can also try temporarily adding an extra fine filter mat into your skimmer to catch pieces of debris too tiny to be caught by standard mats.


    Sludge is the hodgepodge of stuff that sink to the bottom of your pond or collects on your filter mats – usually some mix of decaying leaves, dead algae, fish waste and anything else that doesn’t make it into the skimmer.

    The easiest way to combat sludge is to prevent it:

    • Don’t overfeed your fish.
    • Make sure your biological filtration is big enough to handle the number of fish in your pond.
    • Make sure your skimmer is big enough to handle the amount of debris in your pond. If you don’t have a skimmer, use a net to regularly remove debris.
    • Install a leaf net over the fall.
    • If your pond is prone to sludge, use preventative doses of Sludge & Filter Cleaner to keep it from getting out of hand.

    You’ll probably always have a little bit of sludge in the bottom of your pond and in your filters – and that’s OK. Excessive amounts of sludge, though, can create high levels of ammonia in your pond and cause serious harm to your fish.

    You have two options for removing sludge from your pond: removing it yourself or letting bacteria do the work for you.

    pond sludge and filter cleanerSludge & Filter Cleaner includes special types of bacteria that specifically break down gunk on the bottom of your pond and in your filters. You can – and should – use it in combination with Maintain or regular Beneficial Bacteria to keep algae in-check at the same time.

    If your sludge problem is especially bad, you can remove the sludge manually. Use a net or pond vacuum to get most muck out of the bottom of your pond, and gently rinse your skimmer mats if needed (try to avoid rinsing your biofilter – otherwise you risk turning your water green). The best time to remove sludge from your pond this way is during a spring clean-out, before the beneficial bacteria colonies have established themselves for the season.

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