<p><strong>Abstract.</strong> Given their increasing trend in Europe, an understanding of the role that flooding events play in carbon and nitrogen cycling and greenhouse gas (GHG) emissions will be important for improved assessments of local and regional GHG budgets. This study presents the results of an analysis of the CO<sub>2</sub> and N<sub>2</sub>O fluxes from a coastal grassland ecosystem affected by episodic flooding that was of either a relatively short or long duration (SFS and LFS sites, respectively). Compared to the SFS, the annual CO<sub>2</sub> and N<sub>2</sub>O emissions were 1.4 and 1.3 times higher at the LFS, respectively. Mean CO<sub>2</sub> emissions during the period of standing water were 144&#8201;&#177;&#8201;18.18 and 111&#8201;&#177;&#8201;9.51&#8201;mg CO<sub>2</sub>-C&#8201;m<sup>&#8722;2</sup>&#8201;h<sup>&#8722;1</sup>, respectively, for the LFS and SFS sites. During the growing season, when there was no standing water, the CO<sub>2</sub> emissions were significantly larger from the LFS (244&#8201;&#177;&#8201;24.88&#8201;mg CO<sub>2</sub>-C&#8201;m<sup>&#8722;2</sup>&#8201;h<sup>&#8722;1</sup>) than the SFS (183&#8201;&#177;&#8201;14.90&#8201;mg CO<sub>2</sub>-C&#8201;m<sup>&#8722;2</sup>&#8201;h<sup>&#8722;1</sup>). Fluxes of N<sub>2</sub>O ranged from &#8722;0.37 to 0.65&#8201;mg N<sub>2</sub>O-N&#8201;m<sup>&#8722;2</sup>&#8201;h<sup>&#8722;1</sup> at the LFS and from &#8722;0.50 to 0.55&#8201;mg N<sub>2</sub>O-N&#8201;m<sup>&#8722;2</sup>&#8201;h<sup>&#8722;1</sup> at the SFS, with the larger emissions associated with the presence of standing water at the LFS and during the growing season at the SFS. Overall, soil temperature and moisture content were identified as the main drivers of the seasonal changes in CO<sub>2</sub> fluxes, but neither adequately explained the variations in N<sub>2</sub>O fluxes. Analysis of total Carbon (C), Nitrogen (N), microbial biomass and Q<sub>10</sub> values, indicated that the higher CO<sub>2</sub> emissions from the LFS were linked to the flooding-associated influx of nutrients and alterations in soil microbial populations. These results demonstrate that annual CO<sub>2</sub> and N<sub>2</sub>O emissions can be higher in longer-term flooded sites that receive significant amounts of nutrients and where diffusional limitations due to the presence of standing water is limited to periods of the year when the temperatures are lowest.</p>