Global stream and river greenhouse gas emissions seem to be as large as the oceanic C uptake. However, stream and river emissions are uncertain until both spatial and temporal variability have been quantified. Here we investigated in detail the stream CH4 and CO2 emissions within a hemiboreal catchment in Southwest Sweden primarily covered by coniferous forest. Gas transfer velocities (k600), CH4 and CO2 concentrations were measured with multiple methods. Our data supported modelling approaches accounting for various stream slopes, water velocities and discharge. The results revealed large but partially predictable spatio-temporal variabilities in k600, dissolved gas concentrations, and emissions. The variability in CO2 emission was best explained by the variability in k, while dissolved CH4 concentrations explained most of the variability in CH4 emission, having implications for future measurements. There were disproportionately large emissions from high slope stream reaches including waterfalls, and from high discharge events. In the catchment, stream reaches with low slope and time periods of moderate discharge dominated (90% of area and 69% of time). Measurements in these stream areas and time periods only accounted for <36% of the total estimated emissions. Hence, not accounting for local or episodic high emissions can lead to substantially underestimated emissions.