Methane (CH4) tree stem-atmosphere flux is viewed as a new frontier in the global carbon cycle and may be of great importance. The effect on flux from different tree species, forest ecosystems and seasons is still uncertain. This study aims to investigate how CH4 flux from stems of spruces and birches in a boreal riparian zone in northern Sweden was affected during the spring flood. Spatial and temporal patterns were examined in combination with tree species differences. A closed stem chamber system was applied to estimate CH4 flux from 28 trees during pre-snowmelt and snowmelt conditions. A three-way ANOVA analysis and Tukey´s HSD test was applied to test for main effects and interaction effects from “Field day”, “Distance to the stream” and “Species”. The study revealed that i) there was a significant increase in stem flux over the course of the spring flood while not unequivocal, ii) spruces and birches displayed no significant difference in flux, iii) the distance to the stream had no undisputable significant effect on stem flux. However, a trend in flux variation was observed with distance to the stream. No significant interaction effects were detected. Cumulative seasonal environmental changes or natural variability might explain temporal patterns. Spatial patterns may be connected to hot spots close to the stream. Results for species and interaction effects might facilitate estimations of fluxes in forested ecosystems. Methane flux rates are affected over the course of the spring flood, but further studies are needed to determine the cause for it.