Hypoxia-induced changes in net H+, K+ and O2 fluxes across the plasma membrane (PM) of epidermal root cells were measured using the non-invasive microelectrode ion flux measurement (MIFE) system in elongation, meristem and mature root zones of two barley (Hordeum vulgare L.) varieties contrasting in their waterlogging (WL) tolerance. The ultimate goal of this study was to shed light on the mechanisms underlying effects of WL on plant nutrient acquisition and mechanisms of WL tolerance in barley. Our measurements revealed that functionally different barley root zones have rather different O2 requirements, with the highest O2 influx being in the elongation zone of the root at about 1 mm from the tip. Oxygen deprivation has qualitatively different effects on the activity of PM ion transporters in mature and elongation zones. In the mature zone, hypoxic treatment caused a very sharp decline in K+ uptake in the WL sensitive variety Naso Nijo, but did not reduce K+ influx in the WL tolerant TX9425 variety. In the elongation zone, onset of hypoxia enhanced K+ uptake from roots of both cultivars. Pharmacological experiments suggested that hypoxia-induced K+ flux responses are likely to be mediated by both K(+) -inward- (KIR) and non-selective cation channels (NSCC) in the elongation zone, while in the mature zone K(+) -outward- (KOR) channels are the key contributors. Overall, our results suggest that oxygen deprivation has an immediate and substantial effect on root ion flux patterns, and that this effect is different in WL-sensitive and WL-tolerant cultivars. To what extent this difference in ion flux response to hypoxia is a factor conferring WL tolerance in barley remains to be answered in future studies.