We evaluated the specific strategies of hydrophytes for root O2 consumption in relation to N acquisition and investigated whether the strategies varied depending on the aeration capacity. Aeration capacity of roots is an important factor for determining hypoxia tolerance in plants. However, some hydrophytes possessing quite different aeration capacities often co-occur in wetlands, suggesting that root O2 consumption also strongly affects hypoxia tolerance. We cultivated Phragmites australis with high aeration capacity and Zizania latifolia with low aeration capacity in hypoxic conditions with NH or NO treatment and compared the growth, N uptake, N assimilation and root respiration between the two species. In Z. latifolia grown with NH treatment, high N uptake activity and restrained root growth led to sufficient N acquisition and decrease in whole-root respiration rate. These characteristics consequently compensated for the low aeration capacity. In contrast, in P. australis, low N uptake activity was compensated by active root growth, but the whole-root respiration rate was high. This high root respiration rate was allowed by the high aeration capacity. The O2 consumption-related traits of hydrophyte roots were closely correlated with N acquisition strategies, which consequently led to a compensational relationship with the root aeration capacity. It is likely that this functional linkage plays an important role as a core mechanism in the adaptation of plants to hypoxic soils.