Free-living, sympatric sedentary life stages of hosts and parasites are often adapted to similar environmental conditions. When the environment where these life stages occur is disturbed, both species can decline, causing strong negative effects on the parasitic species. For the highly threatened unionoid mussels with their larval parasitic life stage on fish, habitat degradation may simultaneously affect the conditions for the sedentary host fish eggs and the juvenile mussels in the sediment. This study provides novel information on the effect of sedimentation on the emergence rate of yolk sac fry, and its relation to mussel recruitment in two drainage basins, and is exemplified by the brown trout Salmo trutta, host fish for the threatened freshwater pearl mussel Margaritifera margaritifera. The results imply that turbidity and sedimentation can reduce the survival of trout eggs and yolk sac fry emergence rate regardless of trout strain and drainage basin. The results further suggest that low yolk sac fry emergence rates reduce the potential for mussel infestation and recruitment. The results indicate a year round negative effect of sedimentation, having strong and combined direct and indirect effects on juvenile mussel recruitment. Conservation measures that reduce anthropogenic sediment transportation into streams are a key factor for the conservation of mussels and their host fish.