1. Harvested species population dynamics are shaped by the relative contribution of natural and harvest mortality. Natural mortality is usually not under management control, so managers must continuously adjust harvest rates to prevent overexploitation. Ideally, this requires regular assessment of the contribution of harvest to total mortality and how this affects population dynamics. 2. To assess the impact of hunting mortality on the dynamics of the rapidly declining Baltic/Wadden Sea population of common eiders Somateria mollissima we first estimated vital rates of ten study colonies over the period 1970–2015. By means of a multi-event capture-recovery model we then used the cause of death of recovered individuals to estimate proportions of adult females that died due to hunting or other causes. Finally, we adopted a stochastic matrix population modelling approach based on simulations to investigate the effect of past and present harvest regulations on changes in flyway population size and composition. 3. Results showed that even the complete ban on shooting females implemented in 2014 in Denmark, where most hunting takes place was not enough to stop the population decline given current levels of natural female mortality. Despite continued hunting of males our predictions suggest that the proportion of females will continue to decline unless natural mortality of the females is reduced. 4. Although levels of natural mortality must decrease to halt the decline of this population, we advocate that the current hunting ban on females is maintained while further investigations of factors causing increased levels of natural mortality among females are undertaken. 5. Synthesis and applications. At the flyway scale, continuous and accurate estimates of vital rates and the relative contribution of harvest versus other mortality causes are increasingly important as the population effect of adjusting harvest rates is most effectively evaluated within a model-based adaptive management framework.