Mercury (Hg) exposure may cause a wide range of adverse effects in mammals. A piscivorous apex predator, as the Eurasian otters (Lutra lutra) may accumulate and biomagnify heavy metals and pollutants. Here we investigate the Hg burden in 117 otters from Denmark to evaluate Hg concentrations and risks of health effects. Mercury concentrations ranged between 0.02 and 10.1 μg/g wet weight (ww) in liver tissue and 0.30–40.0 μg/g dry weight in fur. Concentrations in liver and fur in individual otters were highly correlated (P < 0.001). Generalized linear modelling showed that mercury concentrations in both liver and fur increased with age (liver: P < 0.002; fur P < 0.05) and with distance to the marine coastline i.e. towards freshwater habitats (P = 0.0526), and δ¹³C in muscle tissues (P < 0.001). No differences were detected between males and females (P > 0.59) and no correlation were detected between Hg concentration and trophic level (δ¹⁵N) (liver: P = 0.35; fur: P = 0.54). Mercury concentrations in the liver exceeded the No Risk threshold in 15% of the otters, and 25% had levels above the lowest observed effect level of 3.4 μg/g ww that may be associated with adverse effects on the central nervous system. The proportion exceeding these thresholds should therefore be monitored to document possible temporal and spatial trends in Hg exposure and the potential risk to the conservation status of the otter population.