Trace elements in freshwater bivalve shells are widely used for reconstructing long-term changes in the riverine environments. However, Northern Eurasian regions, notably the European Russian North, susceptible to strong environmental impact via both local pollution and climate warming, are poorly studied. This work reports new data on trace elements accumulation by widespread species of freshwater mussels Unio spp. and Anodonta anatina in the Severnaya Dvina and the Onega River Basin, the two largest subarctic river basins in the Northeastern Europe. We revealed that iron and phosphorous accumulation in Unio spp. and Anodonta anatina shells have a strong relationship with a distance from the mouth of the studied river (the Severnaya Dvina). Based on multiparametric statistics comprising chemical composition of shells, water, and sediments, we demonstrated that the accumulation of elements in the shell depends on the environment of the biotope. Differences in the elemental composition of shells between different taxa are associated with ecological preferences of certain species to the substrate. The results set new constraints for the use of freshwater mussels’ shells for monitoring riverine environments and performing paleo-reconstructions.