For mitigation of climate change, all sources and sinks of greenhouse gases from the environment must be quantified and their driving factors identified. Nitrous oxide (N2O) is a strong greenhouse gas, and the contribution of aquatic systems to the global N2O budget remains poorly constrained. In this study, we measured N2O concentrations in a eutrophic coastal system, Roskilde Fjord (Denmark), and combined measurements with statistical modeling to quantify the N2O fluxes and budget in the system over a period of six months. To do so, we collected water at 15 sampling points and measured N2O concentrations along with physico-chemical water quality parameters, e.g. temperature, salinity, dissolved inorganic nitrogen and phosphorus, and silicon. We used mixed-effect regression models to predict N2O concentrations in the water from water quality parameters. We then derived N2O fluxes using well-established equations of N2O solubility and water-atmosphere exchanges. These fluxes were then put in perspective with those measured at the landscape scale by eddy-covariance at a 96 m nearby tall tower, and to those estimated from the agricultural land next to the fjord using Intergovernmental Panel on Climate Change (IPCC) guidelines. N2O concentrations in the Roskilde Fjord ranged between 2.40 and 8.05 nmol l−1. The best fitting model between water parameters and N2O concentrations in water included phosphorus and temperature. We estimated that (i) Roskilde Fjord was a sink of N2O, with a median inward flux of -0.04 nmol m−2 s−1, (ii) while the surrounding median agricultural flux was 0.13-0.18 nmol m−2 s−1, and (iii) the median landscape flux was 0.07 nmol m−2 s−1. All estimates of N2O fluxes were of the same magnitude and consistent with each other. These preliminary results need to be consolidated by further research.