AbstractHealthy populations of salmonids are integral for the functioning of ecosystems and a valuable part of sociocultural identities. Past declines were attributed to anthropogenic stressors, raising concern about the sustainability of populations. Accordingly, many salmonids are listed on red lists and protected by national legislation. One region where salmonid populations are threatened is Northern Spain, the most southern distribution of both the Atlantic salmon (protected under the EU Habitat Directive) and the brown trout. Here, we collated ~700 biomonitoring samples of both species collected across 177 sites over a 10‐year period (2010–2019) to describe ongoing trends in these species and to relate them to site characteristics and potential drivers which may modulate these trends. We showed that both species have declined substantially, with stocked individuals constituting the majority of both populations. Natural reproduction was almost entirely absent for the brown trout (<1%), but present in the Atlantic salmon (~20%). Both species expressed distinct spatial patterns, likely related to their stocking and habitat preferences. As a result, we not only underline alarming conditions of both species, but also question the effectiveness of currently employed stocking efforts. Given that both species are of increasing conservation concern, river basin‐specific analyses are required to identify limiting factors on which conservation actions can be taken. In the evaluated river systems, identified targets include dam removal and pollution reduction, concomitant to the implementation of more effective stocking practices to reduce dependency and maximise conservation benefits for aquatic populations.