Conservation of migratory salmonids requires understanding their ecology at multiple scales, combined with assessing anthropogenic impacts. We present a case-study from over 100 years of data for the endemic landlocked Atlantic salmon (Salmo salar, Salmonidae) and brown trout (Salmo trutta, Salmonidae) in Lake Vänern, Sweden. We use this case-study to develop life history-based research and monitoring priorities for migratory salmonids. In Vänern, small wild populations of salmon and trout remain only in the heavily regulated Rivers Klar (Klarälven) and Gullspång (Gullspångsälven), and commercial and sport fisheries are maintained by hatchery stocking. These populations represent some of the last remaining large-bodied (up to 20 kg) landlocked salmon stocks worldwide. We found that one of four stocks of wild fish has increased since 1996; the other three remain critically low. Hatchery return rates for three of four stocks appear stable at roughly 1% and annual fisheries catch is roughly 75 metric tons, with an estimated 7.5% of hatchery smolts being recruited to the fishery; this also appears relatively stable since 1990. Our analysis reveals much uncertainty in key data requirements, including both river return and fisheries catch rates, estimates of wild smolt production and survival, and hatchery breeding and genetics protocols. These uncertainties, coupled with a lack of information on their riverine and lacustrine ecology, preclude effective management of these unique populations. We conclude with a framework for a life history-based approach to research and monitoring for Vänern salmon and trout, which should be applicable for all endemic, migratory salmonid populations.