In North Carolina, winter weather events causing sea surface temperatures to acutely drop below approximately 12°C may result in strandings of threatened loggerhead Caretta caretta, green Chelonia mydas and endangered Kemp's ridley Lepidochelys kempii sea turtles due to cold stun syndrome. Clinically, these turtles have been shown to have metabolic and respiratory acidosis. The purpose of this study was to apply NMR-based metabolomics to further our understanding of the pathogenesis of cold stun syndrome in sea turtles. Heparinized whole blood and plasma samples were collected from apparently healthy loggerhead (whole blood n = 8), green (whole blood n = 12, plasma n = 10) and Kemp's ridley (whole blood n = 14, plasma n = 10) sea turtles. Blood and plasma samples were also collected from juvenile, in-water or beach-cast cold stun affected sea turtles (loggerhead n = 9, green n = 11, Kemp's n = 6). We identified 18 metabolites in our spectra including amino acids, energy compounds, glycerol, ketone bodies, nucleosides/nucleotides, organic acids and osmolytes. There were several significant differences between metabolites in control and affected turtles, likely secondary to anorexia, such as differences in dimethyl sulfone, glycerol, leucine, isoleucine and trimethylamine N-oxide concentrations. Significant differences in multiple metabolites related to exertion and anaerobic metabolism included concentrations of acetate, creatine, lactate and succinate. Changes in glycerol and propylene glycol concentrations suggest some metabolic changes may have cold protective properties. The primary metabolomic findings were consistent with what is known about clinical biochemistry and blood gas panel perturbations in cold stun affected turtles. This study provides a baseline for the metabolic profile of control and cold stun affected sea turtles in North Carolina and we have identified several metabolites worthy of further investigation with regards to their roles in hypoxia, ischemia and reperfusion.