Biodiesel is increasingly used as a fuel in transportation. It is generally considered an environmentally friendly alternative for diesel from fossil oil, because of lower emissions of the greenhouse gas carbon dioxide (CO2). However, nitrous oxide (N2O) emissions during the growth of energy crops can be considerable. N2O is emitted as a result of fertiliser use, needed to cultivate the energy crops. Fertiliser use not only increases the direct agricultural soil emissions, but also the indirect N2O emissions from aquatic systems, after leaching and runoff of nitrogen from fertilised soils. The aim of this study is to quantify future N2O emissions associated with the cultivation of energy crops in European river basins. We analyse three future scenarios for biodiesel production in Europe, and the associated N2O emissions from fertilised fields. Our focus is on biodiesel produced from first generation energy crops. The scenarios assume that by the year 2050, 15–30% of the demand for fossil diesel is replaced by biodiesel. This would change the European fertiliser needs and, as a result, N2O emissions from fertilised soils. Our results indicate that increased biodiesel production may increase N2O emissions in Europe by about 25–45% relative to a scenario without a growth in biodiesel production, but not equally in all regions and all scenarios. The rate of change depends on where energy crops are grown, and whether or not they replace agricultural crops, or natural vegetation.