Freshwater habitats are beset by a combination of anthropogenic stresses, resulting from a wide array of human activities that occur either within the habitat itself or within the catchment of the habitat. This paper describes the difficulties of making management decisions in fresh waters in the face of this complexity, and outlines the approach adopted by Natural England to counter the problem in a way that allows timely management decisions to protect and restore freshwater sites with special designations for wildlife. The management model outlined has relevance to all those engaged in the management of specially protected freshwater sites, or indeed any type of site suffering from multiple stresses. The approach is also relevant to management models under consideration in England and elsewhere in Europe to fulfil obligations under the EC Water Framework Directive.