The aim of this study was to examine the magnitude of greenhouse gas (GHG) concentrations in tree stems of Pacific Northwest, USA coastal forests and evaluate various tree and site characteristics along river‐to‐sea gradients as possible drivers of tree stem GHG variation. We measured the concentration of CH4, CO2, and N2O during summer and winter in live and dead tree stems of five species from six coastal watersheds and related this to soil porewater GHG concentrations, porewater salinity, and tree characteristics. Overall, average pCO2 and pCH4 were elevated above atmospheric concentration, and average pN2O was slightly below atmospheric concentration. Stem pCO2 was higher in the summer than the winter and was higher in angiosperm trees compared to gymnosperm trees, whereas pCH4 was significantly higher in fresh upstream compared to salt‐influenced reaches. Stem pCH4 was also positively correlated with porewater pCH4 in contrast to other GHGs. The above results suggest that tree stem pCH4 in these coastal settings was primarily controlled by soil linkages, pCO2 was primarily regulated by tree physiology, and factors controlling pN2O remain unclear.