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The study aimed to analyze the dynamics of nitrogen (N) processing along an inundation gradient from floodplain soils to river sediments and identify environmental factors affecting net nitrous oxide (N<jats:sub>2<\/jats:sub>O) production from different microbial sources. Intact soil and sediment cores were subject to two consecutive drying-rewetting cycles in laboratory experiments. The<jats:sup>15<\/jats:sup>N isotope pairing technique was used to quantify N<jats:sub>2<\/jats:sub>O emissions sourced from denitrification and nitrification. We observed enhanced N<jats:sub>2<\/jats:sub>O emissions from both nitrification and denitrification following drying events. Sites exposed to frequent drying-rewetting cycles appear less affected by drying than hydrologically more stable habitats. Fluxes from nitrification were related to the organic matter content, while fluxes from denitrification were controlled by dissolved organic matter quality changes during the drying-rewetting cycles. 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