Locally adapted populations may respond differently to environmental change. Effective management of fish populations therefore requires information on genetic diversity and population structure as well as estimates of population size. However, genetic data are rarely integrated into fisheries governance due to limitations of conventional monitoring methods, leading to decisions based on incomplete information. Environmental DNA (eDNA), consisting of genetic material released into the environment, offers a noninvasive alternative which can be used to generate data on species presence, genetic composition, and potentially provide population-level genetic information and populations size indicators relevant for fisheries management. Focusing on Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) from river systems in southern Sweden, our study assesses the potential of eDNA to infer population structure, genetic diversity, and population size by combining traditional field sampling (electrofishing, fish counter and fish traps), and genetic analyses suitable for eDNA (mitochondrial DNA, single-nucleotide polymorphism, RAD sequencing, metabarcoding, and qPCR estimates).