The freshwater pearl mussel Margaritifera margaritifera is in serious decline in Europe and is protected under the EU Habitats and Species Directive (92/43/EEC). In the Republic of Ireland, most populations require habitat rehabilitation through catchment management in order to secure their future. A series of six filters have been developed to aid prioritisation of measures to be undertaken in order to provide the best return for effort in terms of attaining sustainable populations in favourable conservation status. The results show that prioritisation of the largest populations in the closest to sustainable conditions is of key importance, and that appropriate catchment management measures need to be urgently implemented as there can be a long time delay in the recovery of suitable habitat conditions. The methodology may serve as an example and could be adapted by other countries to produce a scientific rationale for their own prioritisation strategies.