Algae in Lakes & Ponds

Algae control in lakes and ponds can be tricky. We break them down into 3 groups that each have different characteristics and management techniques. And at the end of this page there is a link to a sample management plan for algae.


This is the type of algae that causes green water. Certain types of Blue-green algae can even be toxic. Generally, green water is either an indication of a new pond that hasn`t been established with beneficial bacteria, or a result of a nutrient surplus.

In lakes and natural ponds, green water is almost always a sign of nutrient surplus. Finding the source of the nutrients is absolutely critical in dealing with the problem. Common sources include lawn fertilizers, leaky septic systems, waterfowl droppings, soil erosion, leaves, grass clippings and agricultural runoff. Some solutions to these problems include:

  • Create a buffer zone around the water body (~20 feet out from the shoreline), where long-rooted native vegetation grows to stabilize the shoreline and create permeable soils that will absorb some of the surface runoff. We recommend using a blend of native grasses and wildflowers to develop the vegetation.
  • Hire a professional to diagnose septic problems if there is reason to suspect that it is adding nutrients to the water body.
  • If you must use lawn fertilizer, apply a zero phosphorous product only. The middle number on the fertilizer label is phosphorous, and it needs to be zero, not just a low number. For example, 10-0-10 is a zero phosphorous fertilizer and will make a real difference, but 10-2-10 is not and will not. Do not overlook this step if fertilizer is applied in your watershed area! It is probably the one thing that will make the biggest difference in your pond. 
  • Native Aquatic Plants compete with the algae for the available nutrients in the water.
  • Discourage waterfowl from frequenting the water body. Canada Geese will avoid areas where vegetation prevents them from gaining access to mowed lawns.
  • Use Phosphate Binders/Removers to absorb the nutrients, which will help clean and clear the water.
  • Add an Aeration System to help circulate the water, which brings oxygen down to naturally occurring microorganisms on the pond bottom, where oxygen lacks during the summer.  This will help break down organic matter and help clean and clear the water.
  • Apply Pond Bacteria, which will significantly help the pond process the nutrients. FYI, results will be limited if oxygen levels are low, as most of the beneficial bacteria require oxygen at high levels to do their job.  Therefore, we recommend that you consider an Aeration System before Pond Bacteria.


This is the infamous string or blanket algae. Many different types occur and some of them are resistant to algaecides. Therefore, the best approach is prevention. Here again, as discussed in the planktonic algae section above, the best thing you can do is to find the source of the nutrients and cut it off. This is especially true in large water bodies, like lakes, where chemical treatments cost thousands of dollars. However, no matter how diligent you are at stemming off nutrients, there is usually a certain amount of algae that still grows.

In lakes and natural ponds, the following are the most important steps in dealing with filamentous algae:

  • Prevention. As outlined in the Planktonic Algae section, algae grows because of excess nutrients in the water. Sources of nutrients include fertilizer, soil erosion, tree leaves, grass clippings, leaky septic systems, et cetera. Do whatever you can to stop or minimize nutrients from getting into your water. If you fertilize your yard, either stop or use a zero phosphorous fertilizer.
  • Native Aquatic Plants compete with the algae for the available nutrients in the water. Do not remove them in areas where they do not interfere with your water use.
  • Aeration Systems help the water body clean itself by bringing oxygen to the bottom, where it is often low or absent. This creates aerobic conditions that will help the pond clean itself.
  • Algaecides can be used to kill algae. If the problem is not severe, you may be able to control it with a simple application of EarthTec Algaecide. This product is very user friendly because it self disperses throughout the water column, allowing you to simply pour it into the pond.  However, if you have a significant algae buildup you may be better off applying Cutrine Plus by spraying it directly onto the algae.  Some resistant strains of algae require mixing in a Surfactant and/or Reward Herbicide with the Cutrine Plus to achieve control. Another option is Cutrine Ultra, which is essentially Cutrine Plus with a Surfactant already mixed in.  The downside of Cutrine Ultra is that it ships via UPS Ground Hazardous, which makes it more expensive. Whatever Algaecide that you use, be extremely careful treating ponds that do not have adequate aeration systems, because decaying vegetation uses a large amount of oxygen, which can result in a fish kill. If you do not have adequate aeration and you need to treat algae chemically, only treat 20% of the pond at a time and wait several days between treatments. This will be less effective than full pond treatments, but your fish should survive the treatment (note: ponds with very severe algae problems can suffer oxygen depletion-related fish kills even without any chemical treatments). Use the Pond Calculator to help you calculate acre-feet of water. Also, always check with your states Conservation Department (DNR or like agency) before applying these products to determine if there are any laws restricting their use. Laws vary from state to state. And finally, always read and follow product label instructions.
  • Apply Phosphorous Binders/Removers after algae has been treated to tie up phosphorous released from decaying algae. This greatly reduces the nutrient levels of the pond.
  • You can decrease nutrients in the water by applying Pond Bacteria, which eats sludge and eliminates odors. FYI, results will be limited if an aeration system is not in use, as most of the beneficial bacteria require oxygen at high levels to do their job.
  • Apply a Pond Dye early in the season to inhibit the penetration of sunlight into the water.

Triploid Grass Carp will eat filamentous algae, but they rarely control it because the algae can generally grow faster than the grass carp can consume it. Also, grass carp can increase the algae problem by consuming beneficial aquatic vegetation that competes with filamentous algae for nutrients in the water.

Muskgrass or Chara

This is a bottom-growing form of algae that is commonly confused with weeds. It has a musky odor and a gritty feel to it, which is due to the calcium deposits on its surface. A close relative is called Nitella. These forms of algae can actually be quite beneficial. They cover the bottom and crowd out less desirable species, such as Eurasian Watermilfoil, while filtering the water and providing cover for aquatic organisms. However, if it has grown to a nuisance level or if you are establishing a beach or water-use area, you can effectively control Chara with Cutrine Plus Granular. We highly recommend that you spot treat in the areas where the vegetation interferes with your water use, but leave it be in other areas. By eliminating Chara, you may solve the Chara problem only to replace it with major blooms of Filamentous Algae or something worse, like Watermeal, Eurasian Water Milfoil or Curlyleaf Pondweed!

Triploid Grass Carp are a biological control consideration for Chara. However, partial control is not usually possible with grass carp, and, as stated above, complete removal of Chara can be detrimental to the water quality and the aquatic habitat. Therefore, we generally recommend only spot treating Chara with Cutrine Plus Granular in areas that you want cleared.

More Info on Pond Algae

On our Weed and Algae Management Plan for Ponds and Lakes page we have listed treatment programs for different pond algae problem scenarios that commonly face Koi Pond & Water Garden owners.