Filtration is carried out by forcing algal suspension to flow across a filter medium using a suction pump. The algae biomass is retained and concentrated on the medium and is then harvested. The main advantage of filtration is that it is able to harvest microalgae or algal cells of very low density. A pressure drop must be maintained across the medium in order to force fluid to flow through. Depending on the required pressure drop, various filtration methods have been devised with driving force derived from gravity, vacuum, pressure, or magnetic.

Filtration can be categorized either as surface or deep-bed filtration. In surface filtration, solids are deposited on the filter medium in the form of a paste or cake. Once an initial thin layer of cake is formed on the medium surfaces as precoat, algal cells are deposited on the precoat, serving as a filter medium per se. As algal deposition grows thicker, the resistance to flow across the medium would increase. The filtration flux would decline for a constant pressure-drop operation. In deep-bed filtration, solids are deposited within the filter-bed matrix.

The main problems with using filtration to harvest algae are that the fluid flow is limited to small volumes and by clogging/fouling of the medium by the deposited cells. Several other methods have been devised to avoid filter clogging or membrane fouling. One involves the use of a reverse-flow vacuum in which the pressure operates from above, making the process less vigorous and avoiding algal cell deposition. A second process uses a direct vacuum with a paddle above the filter, providing agitation that prevents the particles from depositing on the medium. Use of a microstrainer as a pretreatment to filtration can reduce clogging and improve algae harvesting. Most filtration operations would include frequent backwashing as a routine maintenance to tackle filter clogging or fouling.

Several filtration methods have been used for algae harvesting with varying degrees of success. The following section discusses various filtration methods that have been used for algae harvesting.