Natural lakes and reservoirs are important yet not well‐constrained sources of greenhouse gasses to the atmosphere. In particular for N2O emissions, a huge variability is observed in the few, observation‐driven flux estimates that have been published so far. Recently, a process‐based, spatially explicit model has been used to estimate global N2O emissions from more than 6,000 reservoirs based on nitrogen (N) and phosphorous inflows and water residence time. Here we extend the model to a data set of 1.4 million standing water bodies comprising natural lakes and reservoirs. For validation, we normalized the simulated N2O emissions by the surface area of each water body and compared them against regional averages of N2O emission rates taken from the literature or estimated based on observed N2O concentrations. We estimate that natural lakes and reservoirs together emit 4.5 ± 2.9 Gmol N2O‐N year−1 globally. Our global‐scale estimate falls in the far lower end of existing, observation‐driven estimates. Natural lakes contribute only about half of this flux, although they contribute 91% of the total surface area of standing water bodies. Hence, the mean N2O emission rates per surface area are substantially lower for natural lakes than for reservoirs with 0.8 ± 0.5 versus 9.6 ± 6.0 mmol N·m−2·year−1, respectively. This finding can be explained by on average lower external N inputs to natural lakes. We conclude that upscaling‐based estimates, which do not distinguish natural lakes from reservoirs, are prone to important biases.