Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2.2 μg CH4 min−1 (whole canopy). Flux increased with temperature. Compared to the isotopic composition of root water CH4, δ13C values were depleted for canopy CH4 where the warmest temperatures (24.4–28.7 °C) resulted in an epsilon of 2.8 ± 4.7 ‰; midrange temperatures (20.4–22.1 °C) produced an epsilon of 7.5 ± 3.1 ‰; and the coolest temperatures (16.0–19.1 °C) produced an epsilon of 10.2 ± 3.2 ‰. From these results it is concluded that there are likely multiple transport processes at work in CH4 transport through trees and the dominance of these processes changes with temperature. The transport mechanisms that dominate at low temperature and low flux result in a larger fractionation, while the transport mechanisms that prevail at high temperature and high flux produce a small fractionation. Further work would investigate what combination of mechanisms are specifically engaged in transport for a given fractionation of emitted CH4.