Classifying Ecological Quality and Integrity of Estuaries

International audienceThere is an increasing need in assessing ecological quality and integrity of estuaries and lagoons as transitional waters. This chapter shows the most recent efforts in assessing individual biological elements (from phytoplankton to fishes), together with the integrative tools developed in different geographical areas worldwide. However, reducing multifaceted information needed to describe complex ecosystems that are naturally stressed from multiple ecosystem elements to a single color or value is a substantial challenge to marine scientists, and requires the integration of different disciplines (chemists, engineers, biologists, ecologists, physicists, hydrologists, managers, etc.), to reach agreement on the final assignment of ecological status. Hence, in the future, emphasis needs to be directed at understanding the complexities of estuarine system functioning rather than simplifying, deconstructing and scaling down the system into smaller components. Indeed, the process of deconstructing an ecosystem for study and then reconstructing it to give a holistic and weighted assessment is by far the greatest challenge in areas where there are many activities, pressures and effects. Key Points • To manage human pressures and impacts on transitional environments, legislation worldwide require methods to assess their ecological status, and here we revise the different methods. • Although methods can address individual ecosystem components (e.g., phytoplankton, macroinvertebrates, fish), inte-grative methods to assess the status under an ecosystem approach are more common in recent times. • Due to the natural variability of estuaries, sometimes distentangling the effects from human pressures and natural stress, can be difficult. • We have reviewed methods to assess the status for phytoplankton, zooplankton, macroalgae, angiosperms, macro-invertebrates, and fish. • Traditional and new methods (e.g., molecular-based methods) are reviewed. • The integration of multiple components, in different geographical areas, is presented