The field of aquatic ecosystem health is a new and developing discipline. The restoration and recovery of habitats is extremely complex and requires a clear understanding of a desirable and maximum/minimum set of conditions which is acceptable, achievable, and cost-effective for implementation. Since this field of research is still in its infancy, the technology for an integrative and innovative assessment will require a combination of physical, chemical, and biological methods and researchers will have to adopt and use some of the routine chemical, limnological, physiological, ecological, and toxicological procedures. A multi-disciplinary, multi-trophic and an ecosystemic approach has been initiated and applied in the North American Great Lakes during the past several years. This strategy, consisting of structural and functional indicators and endpoints, was implemented in the Great Lakes 'Areas of Concern' adopting a field to laboratory approach for a holistic and integrated evaluation of the ecosystem. Some examples from our Great Lakes experience are presented. The ecosystem health technology should look beyond the traditional approach and must develop innovative, sensitive, automated, and cost-effective procedures including computer-assisted techniques to deal with the problems of stress, healing, recovery, and remediation.