Estuaries are important conduits between terrestrial and marine aquatic systems and function as hot spots in the aquatic methane cycle. Eutrophication and climate change may accelerate methane emissions from estuaries, causing positive feedbacks with global warming. Boreal regions will warm rapidly in the coming decades, increasing the need to understand methane cycling in these systems. In this 3-year study, we investigated seasonal and spatial variability of methane dynamics in a eutrophied boreal estuary, both in the water column and underlying sediments. The estuary and the connected archipelago were consistently a source of methane to the atmosphere, although the origin of emitted methane varied with distance offshore. In the estuary, the river was the primary source of atmospheric methane. In contrast, in the adjacent archipelago, sedimentary methanogenesis fueled by eutrophication over previous decades was the main source. Methane emissions to the atmosphere from the study area were highly variable and dependent on local hydrodynamics and environmental conditions. Despite evidence of highly active methanogenesis in the studied sediments, the vast majority of the upwards diffusive flux of methane was removed before it could escape to the atmosphere, indicating that oxidative filters are presently still functioning regardless of previous eutrophication and ongoing climate change.