This paper presents an overview of the possibilities for further development of tools and. approaches for the ecological assessment and management of diffusively contaminated ecosystems. It is based on the results of the "Netherlands Stimulation Programme on Ecosystem-oriented Ecotoxicological Research", the SSEO programme, which ran from 1998 to 2006, and on opinions of international experts on ecological and ecotoxicological risk-assessment methods and their legal applications. The paper also discusses the pros and cons of the set-up of the SSEO programme. Proper management of diffusively polluted areas has to be based on an integral risk-based and system approach. The approach has to be founded on the relationships between pollution, natural stresses, management measures and the presence and activities of specific species. Furthermore, the relationships between biodiversity in ecosystems and its stability and functioning have to be known. The assessment of aquatic ecosystem quality is now based on the comparisons of the composition of actual species with that of reference species. This type of system does not yet exist for the assessment of soil quality, but it is being developed. It is shown that ecological quality criteria based on a Species Sensitivity Distributions approach are sufficiently conservative to avoid or prevent major ecological impacts of diffuse pollution at concentrations below legal standards. However, a proper quality relationship of biodiversity and ecosystem functioning is lacking in the ecological assessment methods. Future research should focus on the relationship of ecosystem structure (species composition) and ecosystem functioning and on the impact of disturbing the environment and appropriate management measures. © 2008 Elsevier B.V. All rights reserved.