In the UK, research funded by the Environment Agency/English Nature has provided a series of spreadsheet-based assessment tools for calculating doses received by biota in coastal, freshwater and terrestrial ecosystems. The approach uses the reference organism concept where the organism of interest (feature species) is equated to a particular reference organism (based on its physical geometry and ecology). This paper describes the stages followed to collate additional species-, and site-, specific data and to undertake assessments to determine whether Natura 2000 sites are adequately protected from authorised releases of ionising radiation. The feature species used for the assessment were species listed under the EC Birds and Habitats Directives. The paper will describe the overall assessment process followed by the UK Environment Agency, demonstrating the staged assessment process adopted; how each feature species is mathematically aligned with the most appropriate reference organism geometry; and provide an example of the assessment conducted for the Natura 2000 sites located in the Humber Estuary, UK.