Abstract. Given their increasing trend in Europe, an understanding of the role that flooding events play in carbon (C) and nitrogen (N) 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 CO₂ and N₂O fluxes from a coastal grassland ecosystem affected by episodic flooding that was of either a relatively short (SFS) or long (LFS) duration. Compared to the SFS, the annual CO₂ and N₂O emissions were 1.4 and 1.3 times higher at the LFS, respectively. Mean CO₂ emissions during the period of standing water were 144 ± 18.18 and 111 ± 9.51 mg CO₂–C m⁻² h⁻¹, respectively, for the LFS and SFS sites. During the growing season, when there was no standing water, the CO₂ emissions were significantly larger from the LFS (244 ± 24.88 mg CO₂–C m⁻² h⁻¹) than the SFS (183 ± 14.90 mg CO₂–C m⁻² h⁻¹). Fluxes of N₂O ranged from −0.37 to 0.65 mg N₂O–N m⁻² h⁻¹ at the LFS and from −0.50 to 0.55 mg N₂O–N m⁻² h⁻¹ at the SFS, with the larger emissions associated with the presence of standing water at the LFS but during the growing season at the SFS. Overall, soil temperature and moisture were identified as the main drivers of the seasonal changes in CO₂ fluxes, but neither adequately explained the variations in N₂O fluxes. Analysis of total C, N, microbial biomass and Q₁₀ values indicated that the higher CO₂ emissions from the LFS were linked to the flooding-associated influx of nutrients and alterations in soil microbial populations. These results demonstrate that annual CO₂ and N₂O emissions can be higher in longer-term flooded sites that receive significant amounts of nutrients, although this may depend on the restriction of diffusional limitations due to the presence of standing water to periods of the year when the potential for gaseous emissions are low.