Removing Brown Diatom Algae From Saltwater Aquariums

Saltwater aquarium


AMR Image/Getty Images

We have all experienced it. You set up your new tank, install all of your live rock and arrange it just right, including the perfect arch in the center of the substrate. Next, the beautiful corals are put in perfect position, so as not to offend each other, and then you carefully acclimate the perfect fish and invertebrates and turn them loose in the tank.

Everything is working wonderfully for about four weeks until all of a sudden everything is covered with a blanket of ugly brown algae. You run another battery of water chemistry tests, which show the same results that they always have: a slight trace of ammonia, zero nitrites, near zero nitrates, and a trace of phosphates. There is little food (nitrates or phosphates) for algae to feed on, so what is this ugly brown stuff, and where is it coming from? A better question is "how do you get rid of it?" No matter what you do, it just seems to keep growing and getting worse all the time. What you are seeing is brown diatom algae, and it is like no other algae--green, red, or brown--that you have ever dealt with before.

Brown Diatom Algae

Diatoms are photosynthesizing (using light to produce its own food) algae, as are many other types of algae. Diatoms are found in the oceans, lakes, ponds, rivers, and even in damp soil and that mud puddle in your backyard. In other words, they are found anywhere there is water. They have a siliceous (containing abundant silica) skeleton capable of only limited movement along a surface area, which they achieve by secreting a mucilaginous (a thick, gluey substance produced by nearly all plants and some microorganisms) material along a groove or channel called a raphe (a groove, ridge, or seam in an organ or tissue).

Brown diatoms are autotrophic (capable of synthesizing their own food from inorganic substances using light or chemical energy) and therefore are restricted to areas that contain some light in order to grow and reproduce. Brown diatom algae can be found in the oceans down to depths of about 600 feet, so they won't have any problems finding enough light to multiply in your brightly lit reef tank which is only 24 inches deep.

Brown diatom algae are algae which form endoplasmic cysts, which store oils rather than starch and secrete silica at some stage of their life cycle.

Masses of diatom skeletons have been preserved on earth in such large quantities that they have formed large deposits that have been (and still are) harvested and used in filters, paints, toothpaste (think about that the next time you're standing in front of the bathroom mirror polishing your pearly whites), and many other applications.

Brown diatoms are almost always seen in new tanks which have just completed their biological cycling process. The algae bloom may be just a skiff of brown on parts of the substrate, rocks, and aquarium walls, or it might be a complete coating. Most aquarists have dealt with this problem by siphoning the diatoms off of the substrate and rocks and brushing it off of the tank walls. Eventually, it went away, hopefully before it did any serious damage to the corals in the tank by covering and suffocating them.

Why Remove Brown Diatom?

There are a number of reasons to remove them from your tank and keep them from reappearing in the future, other than the fact that brown diatoms are ugly in an aquarium.

  • They can deplete oxygen in the tank when they die and decompose.
  • They can cover the corals and live rock, suffocating them and causing die-off.
  • As the diatoms decompose, they release silicates back into the aquarium water.
  • Difficult to remove from the rock and aquarium walls.

Most saltwater aquarists don't stop to think about natural ways to remove brown diatoms from their saltwater tanks. In this day and age of having a variety of chemicals and treatments for every affliction a marine (or freshwater) aquarium experiences, the little creatures that nature has produced which keep brown diatoms from over-running the planet are quickly overlooked.

Years ago, when we were collecting tropical fish on one of the outer islands in Hawaii, we had a number of glass holding tanks with under-gravel filters which produced a lot of algae. Several of the tanks always seemed to have an abundant coating of brown diatoms which always reappeared after each cleaning. Some of the tanks would end up having a number of Kole Tangs (Ctenochaetus strigosus) in them while they were waiting for shipment. It didn't take long for the Kole Tangs to produce a mosaic of little fish lip marks in the brown diatoms on the aquarium walls. They loved the diatoms and would probably have cleaned the whole tank if they had remained for any length of time. Being that the tanks were for simply holding the fish before shipment, the algae wasn't a great concern, but it was impressive how much diatom algae the Kole Tangs consumed in a short period of time.

illustration of how to remove brown diatom algae from aquariums
Illustration: Nusha Ashjaee. © The Spruce, 2018

Dealing With Further Outbreaks

This is pretty much a normal thing for new aquariums to go through. However, if there are further outbreaks of brown diatoms, there is something wrong with the water chemistry in the tank. In the past, we have had several tanks which, for a variety of reasons, have "recycled", generating elevated ammonia and nitrites for a number of days and shortly thereafter produced a short brown diatom bloom which soon resolved themselves. On the other hand, if the tank is not recycling and a substantial brown diatom algae bloom occurs, the problem is probably that there is an overabundance of food in the form of silicates and silicic acid on which the brown diatoms depend to grow.

So, how do the silicates and silicic acid get into your aquarium water? Many water sources (municipal, private, and even wells) contain silicates, silicic acid, or compounds that contain these elements. These compounds eventually break down, leaching silicates and silicic acid that end up in your aquarium. There are a number of silicate test kits available with which you can test your local water to see if it contains silicates.

Check the analysis on the sea salt mix you have been using. Some of these contain a certain amount of silicates, so you might want to consider changing sea salt mixes if you have a continuing problem with brown diatom outbreaks. 

If your freshwater source contains levels of silicates, how do you remove them? Fortunately, there are a number of products that do this fairly efficiently. Before we go into which products will work at removing silicates, let's establish one that will not: activated carbon does not remove silicates, even the highest quality ones. In fact, a number of the lower quality carbon products actually leach phosphates (another brown diatom food) into your water, which is counterproductive.

Many phosphate-removing products also remove silicates from the water at the same time, giving you twice the bang for your buck. Some of these products come in sheet form, some of them in granulated form, and others are already loaded into pad form. Each of these products can be conformed in your filtration system to allow water to run through them, not "over" them. With a little imagination, you will be able to find a way to adapt them to even go in a hang-on filter effectively.

You can also treat your source water to eliminate the silicates. A number of aquarists use RO/DI units to filter their source water. For those who are not familiar with RO/DO units, they are simply a series of chambers that you insert various cartridges into to remove specific compounds and elements from the water. Among the various cartridges available, there are some that will specifically remove silicates. They are not inexpensive by any means and are, for the most part, able to efficiently remove silicates from a few hundred gallons of water before becoming exhausted.

In the end, as you can see, getting rid of and preventing brown diatom outbreaks is not that difficult to do. As with other algae, you just have to remove their food and starve them into oblivion. It's just a matter of identifying their food.