Today, land use impacts a major proportion of all streams. Here, landscape features in corridors along streams and water chemical factors were analyzed in relation to recruitment of the threatened freshwater pearl mussel (Margaritifera margaritifera) and its host fish the brown trout (Salmo trutta). Mussel recruitment and trout density were negatively related to forest clear-cuts. Mussel recruitment was negatively related to water color and turbidity. Therefore, the threats to the mussel may be severe, as low mussel recruitment may be caused by direct effects on the juvenile mussels and indirect effects on the host fish. High proportions of lakes and ponds were found to be positive for recruitment and for trout, and deciduous forest was positively related to trout. The combination of investigations at different scales at the landscape level and at in-stream levels may be applicable to find threats to other threatened species. The results indicate that forestry activities may negatively affect recruitment of freshwater pearl mussels and its host fish. Reductions of forestry activities and the retaining of intact quantity and quality of the riparian zones next to streams, both for the mussel and its host fish may be important conservation measures to restore freshwater pearl mussel populations.