Agriculture is a major source of nitrous oxide (N2O) emissions, a potent greenhouse gas. While direct N2O emissions from soils have been widely investigated, indirect N2O emissions from nitrogen (N) enriched surface water and groundwater bodies are poorly understood. In this contribution, indirect N2O emissions from subsurface agricultural field drains and headwater streams were monitored over a two-year period (2013–2015) in an intensive arable catchment in eastern England. Indirect N2O emission factors for groundwater (EF5g) and surface runoff (EF5r) were calculated for both field drain and streamwater samples, respectively, using two approaches: the N2O–N/NO3–N ratio and the IPCC (2006) methodology. Mean EF5g values derived from the N2O–N/NO3–N ratio were 0.0012 for field drains and 0.0003 for streamwater. Using the IPCC (2006) methodology, the mean EF5g values were 0.0011 for field drains and 0.0001 for streamwater. Thus, EF values derived from both methods were below the current IPCC (2006) default value of 0.0025 and a downward revision to 0.0012 for EF5g and 0.0002 for EF5r is recommended. Such revision would halve current estimates of N2O emissions associated with nitrogen leaching and runoff from agriculture for both the UK and globally.