The Chatham Island Duck, Anas chathamica, is one of many New Zealand bird species that became extinct after Polynesian arrival. The Chatham Island Duck was a large flightless bird, with salt glands on its skull, which led to the hypothesis that it lived in a marine habitat. We tested this hypothesis using a combination of stable isotope analysis (carbon and nitrogen) and analysis of morphoanatomical features. We also conducted a comparative analysis with other anatids from the Chatham Islands and New Zealand. Furthermore, we trialled the non-destructive technique of portable X-ray fluorescence (elemental composition of bones) to assess whether it can be helpful for reconstructing the ecology and habitat of extinct species. We obtained data from museum specimens: 12 samples of A. chathamica and 55 of other anatids for isotope analysis; and 23 samples of A. chathamica and 63 of other anatids for X-ray fluorescence. Results from isotope analysis, supported by anatomical features, show that A. chathamica had a more fully marine diet than previously hypothesised, mainly composed of invertebrates. The large body size of A. chathamica is possibly related to territoriality and combat, which is also supported by the presence of carpal weaponry. Our data demonstrate the importance that the marine environment likely played in the life of this extinct species, while highlighting the key role natural history collections can have in ecological studies.