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This paper develops a decision support system for evaluation of wetland ecosystem management strategy and examines its, so far partial, application in a case study of an important complex coastal wetland known as the Norfolk and Suffolk Broads, in the east of England, UK. Most managed ecosystems are complex and often poorly understood hierarchically organized systems. Capturing the range of relevant impacts on natural and human systems under different management options will be a formidable challenge. Biodiversity has a hierarchical structure which ranges from the ecosystem and landscape level, through the community level and down to the population and genetic level. There is a need to develop methodologies for the practicable detection of ecosystem change, as well as the evaluation of different ecological functions. What is also required is a set of indicators (environmental, social and economic) which facilitate the detection of change in ecosystems suffering stress and shock and highlight possible drivers of the change process. A hierarchical classification of ecological indicators of sustainability would need to take into account existing interactions between different organization levels, from species to ecosystems. Effects of environmental stress are expressed in different ways at different levels of biological organization and effects at one level can be expected to impact other levels, often in unpredictable ways. The management strategy, evaluation methodologies and indicators adopted should also assess on sustainability grounds whether any given management option is supporting, or reducing, the diversity of functions which are providing stakeholders with the welfare benefits they require.