In this study, we analyzed biochemical parameters and the body masses of 14 incubating Common Eiders (Somateria mollissima) breeding on Christiansø in the Baltic Sea from April to May 2015. The eiders were examined and sampled on days 4 and 24, corresponding to early and late incubation. In comparison to reference values, concentrations of alkaline phosphatase (161%), phosphorus (33%), and calcium (44%) were all significantly increased on day 4 by 33–161% due to egg production (p < 0.05). On day 24, we observed a significant loss of body mass (28%) compared to day 4 (p < 0.05). The average plasma concentrations of fructosamine (1-amino-1-deoxy-d-fructose, 21%), amylase (54%), albumin (30%), and total protein declined significantly (all p < 0.05). These declines resemble those seen for other avian species in which the female is the sole incubator, suggesting reduced food intake during the incubation period. A decline in total protein and albumin from day 4 to day 24 (18–30%) is indicative of stage III protein metabolism. Nonetheless, stable concentrations of urea, sodium, and potassium suggest that the incubating females were significantly hydrated. The change in the plasma albumin:globulin ratio from day 4 (0.82) to day 24 (0.57) may imply slight immune suppression, which is supported by the observation of a mass mortality incident shortly after the studied incubation period. These biochemical observations may add to our understanding of the recurrent mortality events that strike without warning in the declining Baltic eider population.