AbstractUpland forest soils are typically major atmospheric carbon dioxide (CO₂) sources and methane (CH₄) sinks, but the contributions of root and microbial processes, as well as their separate temporal responses to environmental change, remain poorly understood. This 2‐year study was conducted in a temperate, deciduous forest located on the Chesapeake Bay in Maryland, USA. We used temporal CO₂ and CH₄ flux measurements, exclusion‐source partitioning, and an ecosystem‐scale flooding experiment to understand how carbon (C) fluxes, and their root and microbial sources, respond to seasonal and episodic environmental change. We show that the root‐and‐rhizosphere component of soil CO₂ and CH₄ flux is significant and that its dependence on soil temperature and volumetric water content (VWC) influences soil C dynamics at seasonal timescales. Experimental flooding shows that CO₂ and CH₄ flux responses to episodic moisture change were driven by suppression of soil heterotrophs, while root respiration did not respond to transient hydrologic disturbance. Methane uptake responded strongly to episodic inundation, reinforcing the important role of soil moisture in the short‐term control of the forest soil CH₄ sink. However, despite the clear seasonality of CH₄ uptake, as well as its strong response to short‐term experimental inundation, temperature and VWC were weak predictors of CH₄ uptake at a seasonal timescale. We suggest that CH₄ consumption in the long‐term may be determined by vegetation, nutrients, microbial communities, or other factors correlated with seasonal changes. Our results indicate that root and microbial sources of both CO₂ and CH₄ flux respond differently in timing and magnitude to seasonal and episodic environmental change.