Plant roots strongly influence C and N availability in the rhizosphere via rhizodeposition and uptake of nutrients. An in situ rhizobox approach was used to compare rhizosphere effects of different tree species and clones on N cycling under seasonally flooded soil. We examined N mineralization and nitrification rates, inorganic N, and microbial biomass C (MBC) and N (MBN) in rhizosphere and bulk soils of three poplar clones, alder, and willow plantations in southeast China. Significant differences in soil pH, total N, soil organic C, MBC, MBN, and MBC/MBN were found between bulk and rhizosphere soils except alder. Compared to bulk soil, the net N mineralization and nitrification rates in rhizosphere soil across all tree species and clones increased by 124–228% and 108–216%, respectively. However, NO₃^–-N was depleted in the rhizosphere soil mainly owing to the root uptake and rhizosphere microbial immobilization. The magnitude of rhizosphere effects on N transformations was considerably different among the tree species studied. Of the tested ones, alder had the greatest rhizosphere effect on N transformation, indicating different capacities of tree species to facilitate N turnover in the rhizosphere.