Unless direct milking of a desired algal product is possible (see Purification for an important example), the first step in microalgae value creation is the isolation (harvesting) thereof from the production medium. There are several techniques available for this, including:
- evaporation (usable in areas where both sunlight and water are abundant)
- filtering over micro screens
- centrifugation (often in combination with micro screens)
- flocculation, using agents like alum, ferric chloride or organic polyelectrolytes
- froth flotation: the water and algae are aerated into a froth, which can be removed easily from the water.

High volume, low value applications like biofuels pose a great challenge since cost- and energy effective isolation procedures are essential. From an energy perspective, flocculation and froth flotation techniques are particularly interesting. Centrifugation is an energy intensive processing step that, if unavoidable, should be optimized for energy efficiency to lower the cost price of the end product. Which technique is best is highly dependent on the algal species involved. In general, research on large scale algae isolation is still in its infancy.

The isolation of individual components from algal biomass is discussed under Purification.

    
Microalgae full of astaxanthin ready for harvesting