Crop productivity is largely affected by abiotic factors such as flooding and biotic factors such as weeds. Although flooding after direct seeding of rice helps suppress weeds it also adversely affects germination and growth of rice itself resulting in poor crop establishment. Barnyard grasses (Echinochloa spp.) are among the most widespread weeds affecting rice, especially under direct seeding. The present work aimed to establish effective management options to control this weed. We assessed the effects of variable depths and time of submergence on germination, seedling growth and carbohydrate metabolism of (a) two cultivars of rice known to differ in their tolerance to flooding during germination and (b) two barnyard grasses (E. colona and E. crus-galli) that commonly infest rice fields. Flooding barnyard grasses with 100-mm-deep water immediately after seeding was effective in suppressing germination and growth. E. colona showed greater reductions in emergence, shoot and root growth than E. crus-galli. Delaying flooding for 2 or 4 d was less injurious to both species. E. colona was also more susceptible to flooding than the flood-sensitive rice cultivar 'IR42'. The activity of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) in rice seedlings was increased by flooding after sowing but with greater increases in 'Khao Hlan On' compared to 'IR42'. The activity of ADH and PDC was enhanced to a similar extent in both barnyard grasses. Under aerobic conditions the activity of ADH and PDC in the two barnyard grasses was down regulated, which might contribute to their inherently faster growth compared with rice. Aldehyde dehydrogenase activity was significantly enhanced in flood-tolerant 'Khao Hlan On' and E. crus-galli, but did not increase in flood-sensitive E. colona and 'IR42' implying a greater ability of the flood-tolerant types to detoxify acetaldehyde generated during anaerobic fermentation. Confirmation of this hypothesis is now being sought.