Brown algae is a common occurrence in a newly set up aquarium.

Frank, Neil. 1996 Control of red algae in the freshwateraquaria, pts. 1 & 2. FAMA 11,12/96.
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are used primarily for dealing with aquarium green water; they have little to no effect on the kinds of algae that grow on the glass, substrate or plants. They are mainly used on ponds.
There are three elements that are directly linked with the growth of algae in aquariums:-
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The reason algae is a plural word is because you can’t really have one alga. Algae are single-celled, nearly microscopic organisms. There are certain exceptions — kelp, for instance, are algae — but the ones we’ll focus on are single-celled. Some are large enough that an individual cell can be viewed with the naked eye, but most are quite tiny. If you’ve ever grown Nitella spp. or Chara spp. in the home aquarium, these are actually algae as well. An individual Nitella spp. cell is quite long and can be viewed in some detail with a magnifying glass. This video from Fluval has some great tips to prevent algae growth in your aquarium.
Photo provided by FlickrControls the main and most persistent types of algae in freshwater aquariums
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Put very simply, algae are a greenish/brownish growth that forms along the walls of your aquarium, or on plants and aquarium decorations. Algae are mostly chlorophyll producing photosynthetic organisms that resemble plants a lot. Contrary to plants, algae are single celled and are therefore not really plants. Excessive algae growth can be very frustrating for aquarists, especially for beginner aquarists and for those that have recently installed stronger lights. Since fish provide enough food for plants to grow, the chlorophyll filled algae too find your aquarium a safe breeding ground. Algae look ugly, and are difficult to eradicate completely. A small amount of algae is a natural part of the ecosystem and can even be an appreciated food source for many fish species. Once a thick carpet of algae forms in your aquarium, they will however begin to compete viciously for all the nutrients that your aquarium can provide. The "Algae Bloom" plagues almost every aquarium at one time or the other. Algae grow fast, especially when there is a regular supply of warm sunlight and rich nutrients.Simon also wonders if very high light levels and iron levels may be the keyto prevention. His question appears to be rhetorical because both of theseparameters are important indicators of plant and algae growing conditions inthe aquarium. Sufficient light is need for good plant growth and generallyspeaking the rate will increase with higher intensity. Actively growingplants will also soak up nutrients from the water column helping to starvealgae. While rooted plants can derive nutrients from the substrate, algaebasically get their food from the water. If nutrients concentrations arereduced in the water column, the algae will suffer.Before we start off, it is necessary to know some inevitable facts about the relationship of an aquarium with algae. If you have an aquarium, then algae are inevitable. Algae can even be beneficial. When nutrient levels are very high in your aquarium, the algae consume the extra nutrients, thus making the water healthier for your fish. Algae also indicate that the ecosystem within your aquarium is healthy. Do not resort to chemical controlling of algae if you can get by with the natural method. If you try to chase away your algae too regularly, you will be causing too much of stress for your fish.The blue-green algae are much more harmful than the green algae types and produce substances that are toxic for fish. Excessive illumination and high nitrate and phosphate levels create an ideal environment for these algae. Fish do not eat blue-green algae and the best way to get rid of these algae is a week of total darkness in the aquarium. Several water changes are also a must to get rid of them.