Modest increases in the concentration of medicarpin, 6-fold in leaves and 4-fold in roots, were observed in alfalfa (Medicago sativa L.) seedlings treated with 1 mM metal salts for 72 h. However, medicarpin-3-O-glucoside-6"-O-malonate (MGM) and formononetin-7-O-glucoside-6"-O-malonate (FGM) levels were up to 50-fold lower in metal-treated compared to control roots. Approximately 10% of the "missing" conjugates could be accounted for in the root treatment solution, where FGM and MGM transiently accumulated prior to their hydrolysis. Time-course studies revealed that total isoflavonoid content (roots plus solution) increased slightly after CuCl2 treatment, whereas the levels of FGM and MGM increased rapidly in alfalfa roots immersed in water. This increase was reduced by aeration. The phenylalanine ammonia-lyase inhibitor L-[alpha]-aminooxy-[beta]-phenylpropionic acid was used to show that immersion of the roots reduced conjugate rates of degradation, which explains their accumulation. In contrast, conjugate rates of degradation were elevated in CuCl2-treated roots, with 50% of the increase being due to hydrolysis. Up to 90% of formononetin and medicarpin produced in response to CuCl2 treatment arose via conjugate hydrolysis. Our results demonstrate that both immersion/anaerobiosis and abiotic elicitation modify isoflavonoid metabolism in alfalfa, and that metal-stimulated accumulation of phytoalexins may arise through the release from preformed stores rather than de novo synthesis.