There are two types of freshwater brown algae: brown algae (diatoms) and brown slime algae (dinoflagellates). Nitrates are a factor either before a diatom outbreak or during a dinoflagellate outbreak. Test the nitrates. If they are high, start lowering the nitrates. Nitrates harbor nutrients these critters like to eat, but diatoms don't need nitrates to exist and thrive. They just need silicates in the water withouut any competition for food. Nitrates might cause them to increase reproductive capacities more so than a food source especially if the system has high nitrates during a diatom population explosion.
Feel the algae. Rub some in between your finger tips. If it's gritty and seems to disintegrate, then most likely is diatoms and the most you can do is remove it manually or get a pleco or other bottom feeder to eat some of it. Diatoms are not bad. It's just the accumulations are unsightly. They will go away on their own.
If the algae is more less slimy and resists disintegration then most likely it is caused by dinoflagellates which aren't really brown. They just give themselves a brown appearance in accumulation. In this case you need to do some small water changes, check nitrates and a pleco or other bottom feeder may help you as well.
Bristlenose plecos, wide mouth plecos, true flying foxes, and otocinclus are some of the more effective plecos for brown algae.
Please note that the above descriptions of brown algae only applies to freshwater. Saltwater brown algae is different.
