AbstractThis paper focuses on the pros and cons of using periphyton (phototrophic biofilms) as monitoring tools in natural and managed aquatic ecosystems. The structural (biomass, community composition) and physiological (pigment composition, photosynthesis) descriptors of periphyton are critically examined to evaluate their use as biological indicators. Different responses of biofilms to physical, chemical and biological disturbances (e.g. extreme water pH and excess nutrients) are discussed. An annotated list of the methods used for monitoring managed aquatic systems using periphyton is given. The range of methods presented includes methods to determine the general state of biofilms/periphyton as well as specific methods in relation to growth or structure. A combination of methods can be made depending on the type of information required.