Algae are called "autotrophic organisms", and this means that they produce their own food by a process called photosynthesis. This process allows for the conversion of carbon dioxide (CO2) and water (H2O) in the presence of light and chlorophyll to create oxygen and simple sugars. This crucial process is responsible for supporting much of the life on this planet. Under conditions of optimum photosynthesis, algae put off large amount of oxygen, clean up the water, as well as provide food for other organisms. Suffice to say that it is a good idea to encourage algae to grow in aquariums for they help to create a more natural and stable environment. 

Some of the more crucial factors that affect the growth of algae are: light, water flow, temperature, nutrient concentrations, and competition (both from other algae, as well as many organisms that might eat or compete with the algae). Lets now consider each of these factors in more detail. Light by far is the most critical factor. Many coral reefs are characterized by having very high levels of light intensity, and so salt water aquariums require large amounts of lighting. The quantity, spectrum, and duration all influence not only what types of algae are present, but their relative abundance. Using traditional fluorescent lights, it is virtually impossible to over light a salt water aquarium. A photo period (the amount of time the light is actually on) of about 12-16 hours a day is good. If there are many lights on an aquarium, it is a good idea to turn them on and off in succession. This will help simulate the natural rise and fall of the sun. Lighting considerations are tank specific and to compute the amount of light required calls for specific numbers (depth, bulb number, organism types et.) For a good review of the pertinent facts see Martin Moe's Marine Aquarium Reference. 

Nutrient concentrations also affect algae populations. Many types of hair algae and slime algae grow in response to excess nutrients (particularly nitrates and phosphates). Coral reefs are especially low in nutrients, this coupled with the vast amounts of herbivores (plant eaters) keeps algae populations low on reefs. Certain macroalgaes require supplements of iron and other trace elements to keep them healthy. Tanks with poor lighting, excess nutrients, and low flow often have excessive amounts of unattractive slime and filamentous algae. Flow affects algae in the following way. Areas of low flow are referred to as stagnant. In these stagnant waters the algae quickly uses up the available CO2 and nutrients and subsequently stop photosynthesizing. Many desirable macro algae require high flow to insure adequate nutrient supply. These algae should appear to be moving in the current. If this is not so, they may be quickly overtaken by other undesirable "low flow" film forming algae . Temperature usually only affects algae communities if it deviates too much (not a problem in temperature controlled tanks).