Effective conservation and species management requires an understanding of the causes of poor population growth. Conservation physiology uses biomarkers to identify factors that contribute to low individual fitness and population declines. Building on this, macrophysiology can use the same markers to assess how individual physiology varies with different ecological or demographic factors over large temporal and spatial scales. Here, we use a macrophysiological approach to identify the ecological and demographic correlates of poor population growth rates in the Cape mountain zebra metapopulation. We use two non-invasive biomarkers: faecal glucocorticoids as a measure of chronic stress, and faecal androgens as an indicator of male physiological status. We found that faecal glucocorticoid concentrations were highest in the spring prior to summer rainfall, and were elevated in individuals from populations associated with low quality habitat (lower grass abundance). In addition, faecal androgen concentrations were higher in populations with a high proportion of non-breeding stallions (where male:female adult sex ratios exceed 2:1) suggesting sex ratio imbalances may intensify male competition. Finally, population growth rate was negatively associated with faecal glucocorticoid concentrations and female fecundity was negatively associated with faecal androgens, indicating a relationship between hormone profiles and fitness. Together, our results provide cross population evidence for how poor population growth rates in Cape mountain zebra can be linked to individual physiological biomarkers. More broadly, we advocate physiological biomarkers as indicators of population viability, and as a way to evaluate the impact of variable ecological and demographic factors. In addition, conservation physiology can be used to assess the efficacy of management interventions for this subspecies, and this approach could inform models of species’ responses to future environmental change.