This data set include the data used in the paper "Nitrous oxide emissions from drying streams and rivers" published in Geophysical Research Letters. Streams and rivers are suffering more extreme and prolonged low flow than those that would naturally occur without human intervention. Stressors on water management include withdrawals for food and energy production, as well as climate change, which is expected to increase the severity, frequency and duration of droughts. The resulting reduction of base flow in many watersheds has relevant worldwide effects on biogeochemical processes in streams and rivers; of particular relevance is the production of nitrous oxide (N2O), a greenhouse gas 300 times more potent than carbon dioxide. Droughts and management-induced low flows may increase N2O emissions potentially causing a positive feedback in response to climate change. This data underline the environmental conditions, e.g., land use, nitrogen availability, stream morphology and flow discharge, that may favor positive feedbacks or, on the contrary, conditions that promote a negative feedback. The paper analyzes these possibilities using a novel scaling law Damköhler-based model supported by synoptic field measurements in two watersheds with contrasting land uses and river network. Our results demonstrate that changes in N2O emissions induced by low flows are scale dependent. At the reach-scale, high nitrate availability due to fertilizer runoff fuels an increase of N2O emissions per stream unit area during low flows in agricultural lands. Conversely, stream reaches draining forested lands may see a reduction in areal emissions due to their hydro-morphological characteristics (less sensitive to change in discharge) and water quality (less nitrate availability). At the river network scale, total N2O emissions depend on channel surface area, which decreases with lower flows, causing total N2O emissions to decrease with decreasing discharge in both watersheds, which imparts a form of climate resilience.