Freshwater mussels, Unionoida, are endangered across the globe due to recruitment failure. In the present study, with general linear mixed models, we investigated the relative effects of biotic (host fish density) and abiotic (water depth, fine sediment, water temperature, and water quality) factors on the recruitment of Margaritifera laevis in 10 streams of Hokkaido, northern Japan. We additionally examined the factors regulating the density of the host fish Oncorhynchus masou masou with general linear models. The proportion of juvenile mussels had a unimodal relationship with the host density, which was the most influential factor among the others examined. The positive relationship between mussel recruitment and host density can be attributed to an increased host fish infection rate. The negative correlation between mussel recruitment and host density at high fish densities may be due to reduced larval growth on host fish that are in poor physical condition. We also found that host fish density was negatively affected by nutrient enrichment. Our results suggest that mitigating water quality degradation to recover host fish density should be prioritized to improve mussel recruitment. Although stock enhancement is effective for increasing the salmon population density, excess stocking can further disturb mussel recruitment.