AbstractClimate change may lead to range shifts, and barriers to such displacements may result in extirpations from previously suitable habitats. This may be particularly important in freshwater ecosystems that are highly fragmented by anthropogenic obstacles, such as dams and other smaller in‐stream barriers. Conservation planning in freshwaters should consider the dynamic effects of climate change and the ability of species to cope with it. In this study, we developed a framework for incorporating climate‐driven dispersal barriers into conservation planning taking into account the medium and long‐term impacts of climate change and species with obligatory interactions. Given that freshwater mussels (Bivalvia: Unionida) are a group of highly threatened organisms dependent on fish hosts to complete their larval development and dispersal, we used Marxan to prioritize areas for their joint conservation in the Iberian Peninsula as a case study. We tested two connectivity scenarios between current and future habitats, (i) unlimited dispersal capacity and (ii) dispersal constrained by artificial barriers, and also identified priority translocation areas for species that were unable to disperse. Accounting for the effects of climate change on species distributions allowed the identification of long‐term conservation areas, but disregarding artificial barriers to dispersal may lead to unrealistic solutions. Integrating the location of barriers allowed the identification of priority areas that are more likely to be colonized in the future following climatic shifts, although this resulted in an additional loss of six to eight features (~5%–7%) compared to solutions without dispersal constraints. Between 173 and 357 artificial barriers (~1.6%–3.3%) will potentially block species dispersal to irreplaceable planning units. Where removal of artificial barriers is unfeasible, conservation translocations may additionally cover up to eight additional features that do not meet conservation targets due to dispersal constraints. This study highlights the challenge of identifying protected areas to safeguard biodiversity under climate change.