The method concerning in vivo proton HR-MAS NMR metabolic profiling of the freshwater cladoceran Daphnia magna is presented. Viability tests of D. magna under different spinning rates were performed. All surviving daphnids after analysis have developed eggs and embryos like control animals. Better survival rate at the slowest rotation speed were observed. The maximum length of analysis during which the integrity of the daphnid is maintained was assessed. The recorded proton spectra of in vivo daphnia were attributed to lipids from the triglycerol category. Saturated and unsaturated omega-3 like fatty acid moieties of triacylglycerol were well identified. The relationship between physiological state of daphnids and lipid profile are discussed.