Indigenous crayfish species (ICS) are under threat in Europe; due to competition from invasive non-indigenous crayfish species (NICS) from crayfish plague, which is carried by introduced American crayfish, and habitat degradation. We focus on the white-clawed crayfish Austropotamobius pallipes and stone crayfish A. torrentium. Surveys in many countries have shown the accelerating rate of loss since the late 20th century; concurrent with rapid spread of NICS by human-assisted introductions and natural expansion. Remaining populations of ICS are becoming fragmented. As NICS become ever more extensive, it will become progressively harder to retain populations of European ICS. Legal protection alone is not sufficient against the major threats from NICS and crayfish plague. We recommend catchment-scale risk assessments, to identify threats and to guide action plans: (1) populations of ICS where loss is inevitable, (2) those at some risk that can be made more secure by various measures and (3) existing or new isolated populations that can be kept secure, “ark sites”. Resources can be targeted to achieve specific conservation goals. Ark sites are likely to offer the best chance for survival of both Austropotamobius species, where there are invading NICS. We discuss constraints and opportunities and the need for public involvement.