Five freshwater marsh plant species exhibited different root metabolic responses when flooded to three water depths in field macrocosms. The capacity for alcoholic fermentation (as indicated by alcohol dehydrogenase activity) increased and remained at a relatively high level in the roots of the least flood-tolerant species, Scolochloa festucacea, but was not stimulated significantly or only temporarily in the more tolerant species, Scirpus acutus, Scirpus validus, Typha glauca, and Phragmites australis. During the first month of flooding, alcohol dehydrogenase activity showed a positive relationship with flooding depth and a negative relationship with soil redox potential. Malate accumulated in the roots of S. acutus, S. validus, and to a lesser extent in P. australis in response to flooding; concentrations showed a significant positive relationship with water depth and a significant negative relationship with soil redox potential during the first month of flooding. Differences in root metabolism among the five species were still evident after 1 year of continual flooding. Root specific gravities and air space cross-sectional volumes demonstrated potential species differences in root resistance to oxygen movement and root oxygen volume, respectively. The results suggest that the observed metabolic response reflected differential aeration of the roots resulting from differences in root structure and soil oxygen demand (reducing power).