Atmospheric nitrogen (N) deposition has had detrimental effects on species composition in a range of sensitive habitats, although N deposition can also increase agricultural productivity and carbon storage, and favours a few species considered of importance for conservation. Conservation targets are multiple, and increasingly incorporate services derived from nature as well as concepts of intrinsic value. Priorities vary. How then should changes in a set of species caused by drivers such as N deposition be assessed? We used a novel combination of qualitative semi-structured interviews and quantitative ranking to elucidate the views of conservation professionals specialising in grasslands, heathlands and mires. Although conservation management goals are varied, terrestrial habitat quality is mainly assessed by these specialists on the basis of plant species, since these are readily observed. The presence and abundance of plant species that are scarce, or have important functional roles, emerged as important criteria for judging overall habitat quality. However, species defined as 'positive indicator-species' (not particularly scarce, but distinctive for the habitat) were considered particularly important. Scarce species are by definition not always found, and the presence of functionally important species is not a sufficient indicator of site quality. Habitat quality as assessed by the key informants was rank-correlated with the number of positive indicator-species present at a site for seven of the nine habitat classes assessed. Other metrics such as species-richness or a metric of scarcity were inconsistently or not correlated with the specialists' assessments. We recommend that metrics of habitat quality used to assess N pollution impacts are based on the occurrence of, or habitat-suitability for, distinctive species. Metrics of this type are likely to be widely applicable for assessing habitat change in response to different drivers. The novel combined qualitative and quantitative approach taken to elucidate the priorities of conservation professionals could be usefully applied in other contexts.