Brown "algae" really isn't algae. I will go into details later... but the tanks being next to the window isn't a good idea. Forgetting about the fact that there could be drafts and temperature swings by a window, algae is bound to grow where there is light + water + nutritients to grow.
Types of Algae
Green Surface Algae
Green surface algae is the most common algae found in tanks. It creates a thin layer of hard to remove, dark green algae. Algae-eating fish and snails prefer this type of algae. It can be physically removed but can be difficult. It usually needs to be scraped off.
Brown algae:
Brown algae are actually diatoms and not true algae. They coat ornaments, real and fake plants, glass, and gravel with a thin, dark brown layer. Brown algae prefer low light levels. They commonly grow in new tanks or those with low levels of light. Increasing the intensity or quantity of lights may decrease the growth of brown algae but in turn will increase the growth of other algae. Brown algae is easy to physically remove with an algae pad as it does not adhere as strongly as green algae. While some snails and algae-eating fish will inadvertently eat some brown algae, most algae-eating fish prefer green algae and will only eat brown algae if they have no alternative food source.
Blue-green algae:
Blue-green algae (BGA) are not true algae. They are cyanobacteria. If objects in the tank are coated with thick sheets of slimy, bright-greenish blue algae, it may be blue-green algae. It commonly grows in tanks with too many nutrients. Scrubbing it off and then doing a 50% water change should help. Do frequent large water changes until it goes away. Reduce the quantity of fish or food added. The treatment with antibiotics may kill some or all of the blue-green algae but could also kill good bacteria. When the treatment is ended, the blue-green algae may return. This stuff is nasty! It is a beautiful green but slimy and coats everything once it takes over.
