This review presents environmental and biological indicators of the impact of three major categories of inputs in coral reef lagoons i.e. particles, nutrients and metals. Information was synthesized to extract well established indicators together with some interesting new concepts currently under development, and to provide the reader with an assessment of their respective advantages and drawbacks. The paper has been organized according to the capacity of three categories of indicators to respond either in a specific or a non specific way to a given source of input. The first section focuses on abiotic indicators which main interest is to respond instantaneously and in a truly specific way to a given source of input. The second and third sections present informations on bioindicators either at the sub-individual level or at the individual to community level, indicator specificity generally decreasing as a direct function of biological or ecological complexity. This review showed that even though significant work has already been done on coral reef ecosystems, much more scientific studies are still needed to answer the growing local demands for simple and truly validated tools to be used in environmental surveys. It is further stressed that, due to the biological and environmental diversity of coral reef lagoons, a preliminary step of on-site validation must be considered as an absolute prerequisite when indicators are planned to be used in the frame of a local environmental monitoring programme.