Freshwater mussel (order Unionida) is one of the groups of freshwater molluscs having complex life histories that require temporary parasitization on host fish. They have important ecological functions in freshwater ecosystems but became one of the most imperiled organisms worldwide. One of the important challenges for the conservation of freshwater mussels is determining the processes of recruitment failure, i.e. low levels or no signs of recent joining of juvenile mussels. A series of observational and experimental studies focusing on multiple life-stages determined the population status and demonstrated the processes of recruitment failure of long-lived endangered freshwater pearl mussel Margaritifera togakushiensis in the rivers of eastern Hokkaido, northern Japan. We demonstrated that reduced survival rate of experimentally provided juvenile abundance was associated with the amount of fine suspended sediment, the level of dissolved nutrients, and their interaction. Although there were no clear relationships between suspended sediment levels and agricultural land proportions in catchments, the negative impacts of catchment agriculture were inferred as a cause. Furthermore, the lack of the potential number of juvenile supplies at the parasitic stage can cause recruitment failure interactively with juvenile survival rate. These results suggest that recruitment of M. togakushiensis is limited by multiple life-stage processes.