Physiological effects of flooding might be interpretable through measures of photosynthesis and respiration in plants. Photosynthesis and respiration processes were measured in Phalaris arundinacea L. (reed canarygrass), Phaseolus vulgaris L. (common bean). Pisum sativum L. (pea), Vicia faba L. (broad bean), and Zea mays L. (maize) following three days of flooding. From this, we propose a model of physiological flooding tolerance regarding photosynthetic and respiratory metabolism. Tolerance to flooding results from an ability to maintain photosynthesis and high stomatal conductance when flooded, and to avoid oxygen shortage in roots. The most flooding-tolerant attributes were observed in the wetland grass Phalaris arundinacea. Oxygen was not limiting for root respiration when flooded, and photosynthetic rates and stomatal conductance increased in the flooding treatment. The flooding tolerant Zea mays and the broad bean Vicia faba were the next most flooding tolerant, as indicated by increased photosynthesis rates and stomatal conductance with flooding, but both displayed signs of oxygen stress from three days of flooding. The flooding-sensitive Phaseolus vulgaris and Pisum sativum were the most impacted by flooding, particularly P. vulgaris. Roots of P. vulgaris and P. sativum experienced oxygen stress in flooded treatments. Photosynthesis and stomatal conductance decreased in flooding treatments, and there was evidence of increased photoprotection with flooding in P. vulgaris. An ability to allocate light energy to photochemistry during flooding also appeared to be related to flooding tolerance. Plant flooding tolerance is mainly determined by an ability to maintain respiratory processes in affected tissues.