Boreal rivers and streams are known as hot spots of CO2 emissions, yet their contribution to CH4 emissions has traditionally been assumed to be negligible, due to the spatially fragmented data and lack of regional studies addressing both gases simultaneously. Here we explore the regional patterns in river CO2 and CH4 concentrations (pCO2 and pCH4), gas exchange coefficient (k), and the resulting emissions in a lowland boreal region of Northern Québec. Rivers and streams were systematically supersaturated in both gases, with both pCO2 and pCH4 declining along the river continuum. The k was on average low and increased with stream order, consistent with the hydrology of this flat landscape. The smallest streams (order 1), which represent < 20% of the total river surface, contributed over 35% of the total fluvial greenhouse gas (GHG) emissions. The end of winter and the spring thaw periods, which are rarely included in annual emission budgets, contributed on average 21% of the annual GHG emissions. As a whole, the fluvial network acted as significant source of both CO2 and CH4, releasing on average 1.5 tons of C (CO2 eq) yr−1 km−2 of landscape, of which CH4 emissions contributed approximately 34%. We estimate that fluvial CH4 emissions represent 41% of the regional aquatic (lakes, reservoirs, and rivers) CH4 emissions, despite the relatively small riverine surface (4.3% of the total aquatic surface). We conclude that these fluvial networks in boreal lowlands play a disproportionately large role as hot spots for CO2 and more unexpectedly for CH4 emissions.