Aquatic ecosystems are an important and often understudied part of terrestrial carbon budgets. Streams and rivers emit carbon dioxide (CO2) and methane (CH4) to the atmosphere. CO2 and CH4 concentrations and emissions are controlled by several local stream characteristics, including temperature, channel slope, groundwater inputs and surrounding vegetation type. These state factors vary among streams of different sizes and watershed and climate features; yet, few studies have carried out large cross-biome scale comparison of carbon greenhouse gas concentrations among similar size streams. Here we assessed the variability of CO2 and CH4 in ice-free streams among three biomes: boreal (Quebec, Canada), temperate (New Hampshire, USA), and tropical (Puerto Rico). We analyzed riverine CO2 and CH4 concentrations across 200 streams, varying in stream order from 1st to 6th. We compared surface water CO2 and CH4 concentrations and ratios to assess how the scaling relationships between the two gases varied across stream sizes and biomes. We observed the highest CH4 concentrations in the boreal streams, but average CH4 concentrations were greatest in temperate streams. The scaling relationship between concentrations of CO2 and CH4 were generally positively related with the steepest slopes in boreal streams. Slopes and intercepts of the CO2 vs. CH4 relationships varied systematically across biomes and sites suggesting variable controls of riverine CO2 and CH4 across space.