Diatoms

• Diatoms are unicellular organisms with a silicon shell and brown chloroplasts, giving them a color that is generally not sought-after by aquarium owners, and covering up other, more aesthetic features in the aquarium. There are numerous species of diatoms, and most are found in fresh water, though a few inhabit salt water. They make their energy from light, so they thrive anywhere there is water and a light source. Diatoms reproduce quickly and form chains that become colonies, which accounts for the way they spread in your aquarium.
  
  

Nitrates

• Sometimes called "brown algae," diatoms require nitrates. Sudden outgrowth of brown algae, while in itself not harmful, may indicate other problems in your aquarium. Nitrates are produced from fish waste, from fish food that rots uneaten in the tank and from dead matter left by aquarium plants. Algae blooms indicate sudden spikes in nitrate levels. A sudden, subsequent drop in nitrates can lead to the diatomic algae itself dying en masse, whereupon the decomposition of the algae de-oxygenates the water and stresses or even kills fish.
  
  

Algaecides

• One problem aquarium owners encounter is their own reaction to these brown spots. Owners put algaecides in the fish tank to kill the diatoms. These chemicals also kill off beneficial algae (all aquariums need some algae) and beneficial bacteria. The sudden death of the algae causes de-oxygenation, and the various chemicals used in algaecides will do everything from make your water sudsy to killing plants to killing other animals, such as snails. Moreover, in a few days, algae will return.
  
  

Conrolling Brown Algae

• Brown algae can be controlled by a variety of measures. Aquarium owners can begin by using distilled water instead of tap water to refill aquariums. Tap water often contains silicates, which promotes diatomic reproduction. Aquarium sand is also a silicate culprit, so exchanging sand for gravel can reduce diatom algae. Filter additives are also used to reduce silicates in the water. Many well-balanced aquariums incorporate algae-eating fish and snails to control all algae growth, and live plants hold down the levels of nitrate that contribute to algae blooms.