ABSTRACT Understanding the stable hydrogen isotope (δ 2H) composition and fractionation in lipid biomolecules of primary producers, such as terrestrial and aquatic plants, is crucial for deciphering past environmental conditions, as well as applying compound-specific stable isotope analysis for the study of metabolic and ecological processes. We conducted a new tracer experiment to explore the δ 2H composition of algal fatty acid biomarkers, focusing on freshwater algae, which form the base of aquatic food webs. We selected a range of algal species widely found in freshwater ecosystems and cultivated them under controlled conditions. First, we added 2H2O to ambient water as a tracer to investigate the net hydrogen isotope fractionation during algal lipid synthesis at isotopic equilibrium, which is particularly informative for paleo-geochemical studies. Then, we conducted kinetic experiments to quantify the time needed for algal fatty acids to achieve isotopic steady-state conditions in response to the change in ambient water δ 2H values. Our findings revealed substantial variability in hydrogen isotope fractionation among different algal taxa and various fatty acids. Based on taxa, different fatty acids exhibited faster integration of water hydrogen than others, but they were not necessarily in the order of the biosynthetic pathway. This experiment underscores the complexity of hydrogen isotope fractionation and the requirement for controlled laboratory studies to properly apply compound-specific stable H isotope analysis techniques in ecological and paleo-environmental studies.