The importance of waterlogging in saltmarshes, and especially its role in small-scale patterning, are little known. A physiological/chorological approach was taken to investigate this in a New Zealand salt meadow. The effect of waterlogging on the activities of enzymes associated with anaerobic metabolism, especially alcohol dehydrogenase (ADH), was investigated in a greenhouse experiment with five representative salt meadow species: Puccinellia stricta, Isolepis cernua, Samolus repens, Selliera radicans and Triglochin striata. All species showed a significant increase in ADH activity in either shoots or roots in response to waterlogging. In P. stricta, sucrose synthase and four out of the five enzymes involved in fermentation increased under waterlogging. However, the photosynthetic efficiency (Fv/Fm) of the species did not change under this regime. The species composition gradient on the saltmarsh was related primarily to elevation, a proxy for water inundation, and the distribution of species along that gradient was related to their tolerance of waterlogging as measured by stimulation of ADH activity. However, the species-composition gradient was also related to water-ponding depressions, demonstrating the role of microtopography, with depression mimicking higher elevations, probably due to rainwater ponding.