We investigated variation in adrenal activity in the dugong, a vulnerable cryptic marine mammal species, in a population inhabiting the lower thermal limit of their range. We sampled 319 live wild dugongs and examined faecal glucocorticoid (fGC) concentrations in relationship to sex, reproductive state (immature, sexually mature, or pregnant), and season, as well as associations with body condition, male-induced aggressive conspecific interactions, and environmental temperature. Physiological validations with apparently healthy and unhealthy animals indicated that fGC levels reliably reflect adrenal activation in dugongs. Glucocorticoid levels and body condition varied seasonally, with individuals expressing lowest fGC levels and an improving body condition over summer and autumn. Best body condition was observed in winter, which may have enhanced the ability of the animals to cope with thermal and nutritional challenges and helped to sustain the subsequent costs of reproduction (including mating activity in spring). Immature dugongs, especially those recently estranged from their mothers, may be particularly vulnerable to stress during winter, and also at risk of injury from adult conspecifics. During the spring mating period, mature and sexually active males with large erupted tusks had high fGC and poorer body condition compared with all dugongs, except pregnant females, in all other seasons. This finding was consistent with high levels of body scarring on adults of both sexes, resulting from agonistic behaviour by mature males. Competitive reproductive behaviour, inherent in a promiscuous mating system, may have stressful consequences for male dugongs, especially given that strenuous mating activity follows unfavourable thermal and nutritional conditions. Overall, fGC levels appear to be a good proxy for stressors in dugongs associated with season and/or temperature, intra-specific aggression, and pregnancy, but not lactation and/or maternal care. Understanding baseline fGC levels will allow wildlife managers to identify additional and/or unusual stressors that may threaten wild dugong populations.