<p>Stable isotope analysis serves as a critical tool for understanding ecosystems by providing complex information regarding ecological niches and food web structure. These techniques have served as a principal means for investigating energy flow in food webs supported by submerged aquatic vegetation. Macrophytes structure the food webs they support through multiple energetic pathways, including those from live tissue and detrital matter. However, current stable isotope methods often lack the means to distinguish the relative importance of living and detrital energy pathways in structuring these food webs. We conducted a field experiment to quantify the effect of decomposition on hydrogen (δ²H), carbon (δ¹³C), and nitrogen (δ¹⁵N) stable isotopes in three abundant seagrass and macroalgae species. Decomposition enriched or depleted hydrogen and carbon stable isotopes depending on macrophyte species. Furthermore, hydrogen improved the ability of discriminant models to distinguish among macrophyte species and decomposition stage by 7%. Hydrogen, in combination with other isotopes such as carbon and nitrogen, represents a potentially effective tracer for quantifying the relative contributions of living and detrital macrophyte resources to food webs. Future studies aimed at quantifying the behavior of hydrogen in biotic pools will provide further insight into the utility of this isotope in understanding energy flow and structure of marine ecosystems.</p>