White-clawed crayfish, bullhead, and freshwater pearl mussel are different model organisms in terms of biological traits. Analysing their distribution patterns, habitat demands, and causes of decline may thus help to derive broader frameworks for conservation projects. This paper includes a wide-ranging literature review for these three threatened freshwater animals, then uses general patterns to make suggestions about broader protection measures for freshwater species. Each species has a patchy distribution, from local to broad spatial scales. However, we point out the difficulty to summarise such knowledge, because many variables were not consistently and/or accurately recorded by workers, and because the range of colonised habitats depends on the environmental heterogeneity within study areas. Causes of decline are chiefly related to human activities which modify the biological, chemical, and physical features of the aquatic environment, and can be classified into four types: physical habitat alterations, interspecific interactions, overfishing and poaching, and natural disturbance. By analysing causes of decline and possible actions, we develop seven general trends that could be adopted for a wider array of species. However, protection plans cannot be effective without actual collaborations between river managers, local inhabitants, and authorities. Finally, the re-introduction procedure itself (if needed) depends on the biology of the species under survey, and remains specific. At the same time, further fundamental research is needed to generalise relationships between population and habitat dynamics at different spatial and temporal scales.