Greenhouse gas (GHG) emissions from riparian zones affect the global GHG balance, contribute to global warming and climate change, and generate adverse effects on ecological health as well as environmental, economic and social sustainable development. However, the influence of water-level fluctuations on depth-dependent soil properties, nitrogen transformation and GHG emissions in riparian zone ecosystems during wetting–drying cycles remains unclear. In this study, we analyzed seasonal nitrogen dynamics under seasonal water-level fluctuations at seven different depths (0–20, 20–40, 40–60, 60–80, 80–100, 100–120 and 120–140 cm) along a typical transect in the Jianghan Plain, Central China for 2018–2019. Changes in depth-dependent soil physical and chemical properties, soil textural characteristics and mineralogy, potential nitrification rate (PNR) and potential denitrification rate (PDR), as well as soil GHG emission rates were determined across a range of meteorological conditions and surface water and groundwater level fluctuations. Groundwater levels varied significantly between seasons with rising water-levels during the wet seasons and falling water-levels during the dry seasons. The physicochemical properties and chemical composition in the three studied riparian soil textures revealed higher spatiotemporal variability during the wet seasons as compared to the dry seasons. Our results showed that groundwater level depth was a crucial influencing factor controlling the microbial nitrogen transformation in the soil profiles. The PNR values were characterized by substantial seasonal variation with the same or higher metabolic activity in the dry season than in the wet season owing to water-level fluctuations, while they declined with depth. Compared to the wet season, the PDR values in the studied riparian zone were typically lower in the dry season due to extremely low soil water content constrained by fluctuating water-levels. Besides, the PDR values in the silt loam layers were higher than that in the sandy loam layer for most of the monitoring period. The depth-dependent GHG flux rates highlighted that the riparian zone ecosystem was a key source of CO2 and N2O and a sink for CH4. In summary, our findings suggest that fluctuating water table management in riparian ecosystems must be considered to more effectively control seasonal fluctuations of nitrogen dynamics and mitigate GHG emissions. Thus, a suitable riparian groundwater quality control and management scheme is urgently necessary to bring awareness of seasonal water-level fluctuations of riparian zones to catchment managers and policy makers.