Abstract Multiple stressors can affect populations interactively. However, the process by which they affect recruitment remains unclear, especially in long‐lived organisms with complex life cycles. This study explored the bottleneck stages of juvenile recruitment in the endangered freshwater pearl mussel Margaritifera togakushiensis and the interactive effects of nutrients and fine sediments on these stages. The proportion of M. togakushiensis juveniles aged ≤10 years was investigated in 24 rivers from north‐eastern Japan. Margaritifera togakushiensis has a complex life cycle with an obligate parasitic larval stage. Gravid female density, glochidia density (the number of glochidial infections per stream area), and juvenile survival rate, used as indices for adult, parasitic, and post‐parasitic juvenile stages, respectively, were obtained from 11 of these rivers. Twenty‐four population status assessments showed that the proportion of juveniles aged ≤10 years ranged from 0.00 to 0.23, and that they were absent in 12 rivers. Parasitic and post‐parasitic juvenile stages were bottlenecks for recruitment; juvenile survival rates had a stronger positive effect on recruitment in rivers with high glochidia density. Juvenile survival rate was negatively associated with the synergistic effects of nutrients and fine sediments, although factors limiting glochidia density were not identified. These findings suggest that the interaction between nutrients and fine sediments can synergistically reduce the recruitment of M. togakushiensis, indicating an underestimated impact of stressors on mussel recruitment if treated individually. Future mitigation measures should consider both nutrient levels and fine sediments to restore mussel recruitment. These results also emphasize the importance of considering both parasitic and post‐parasitic juvenile stages of mussels to maximize the success of future restoration actions.