This will help simulate the natural rise and fall of the sun. For a good review of the pertinent facts see Martin Moe's Marine Aquarium Reference. Nutrient concentrations also affect algae populations. 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.