Abstract. Nitrogen retention efficiency in natural Mediterranean wetlands affected by agricultural runoff was quantified and the effect of season and hydrological/chemical loading was examined from March 2007 to June 2008 in two wetland-streams located in Southeast Spain. Nitrate-N (NO3−-N), ammonium-N (NH4+-N), total organic nitrogen-N (TON-N) and chloride (Cl−) concentrations were analyzed to calculate nitrogen retention efficiencies. These wetlands consistently reduced water nitrogen concentration throughout the year with higher values for NO3−-N (72.3%), even though the mean values of inflow NO3−-N concentrations were above 20 mg l−1. Additionally, they usually acted as sinks for TON-N (45.4%), but as sources for NH4+-N. Over the entire study period, the Taray and Parra wetlands were capable of removing a mean value of 1.6 and 0.8 kg NO3−-N a day−1, respectively. Retention efficiencies were not affected by temperature variation and did not follow a seasonal pattern. The temporal variability for NO3−-N retention efficiency was positively and negatively explained by the net hydrologic retention and the inflow NO3−-N concentration (R2adj=0.832, p<0.001), respectively. TON-N retention efficiency was only positively explained by the net hydrologic retention (R2adj=0.1997, p<0.05). No significant regression model was found for NH4+-N. Finally, the conservation of these Mediterranean wetland-streams may act as a tool to not only improves the surface water quality in agricultural catchments, but to also achieve a good ecological status for surface waters, this being the Water Framework Directive's ultimate purpose.