Periphyton widely exists in natural water bodies, with the characteristics of huge biomass generation, strong ecological function, and sensitive response to water quality. It removes the pollutants in water bodies mainly through the processes of absorption, metabolism, adsorption, and complexation, etc. Owing to its high tolerance against pollution and high removal efficiency for nitrogen and phosphorus, as well as the feasibility of recycling its cells at low cost, periphyton is a promising candidate for developing the treatment techniques of water purification. The newly-developed artificial periphyton systems, e.g., algal turf scrubbers, periphyton biofilm systems, periphyton aquaculture systems, have been successfully applied in treating livestock manure, aquaculture wastewater, and municipal sewage. However, further researches are needed to understand the growth patterns of periphyton, its physiological responses to pollutants concentration, and its molecular biological mechanisms in removing pollutants.