Molecular hydrogen (H2 ) is an atmospheric trace gas with a large microbe-mediated soil sink, yet cycling of this compound throughout ecosystems is poorly understood. Measurements of the sources and sinks of H2 in various ecosystems are sparse, resulting in large uncertainties in the global H2 budget. Constraining the H2 cycle is critical to understanding its role in atmospheric chemistry and climate. We measured H2 fluxes at high frequency in a temperate mixed deciduous forest for 15 months using a tower-based flux-gradient approach to determine both the soil-atmosphere and the net ecosystem flux of H2 . We found that Harvard Forest is a net H2 sink (-1.4 ± 1.1 kg H2 ha-1 ) with soils as the dominant H2 sink (-2.0 ± 1.0 kg H2 ha-1 ) and aboveground canopy emissions as the dominant H2 source (+0.6 ± 0.8 kg H2 ha-1 ). Aboveground emissions of H2 were an unexpected and substantial component of the ecosystem H2 flux, reducing net ecosystem uptake by 30% of that calculated from soil uptake alone. Soil uptake was highly seasonal (July maximum, February minimum), positively correlated with soil temperature and negatively correlated with environmental variables relevant to diffusion into soils (i.e., soil moisture, snow depth, snow density). Soil microbial H2 uptake was correlated with rhizosphere respiration rates (r = 0.8, P < 0.001), and H2 metabolism yielded up to 2% of the energy gleaned by microbes from carbon substrate respiration. Here, we elucidate key processes controlling the biosphere-atmosphere exchange of H2 and raise new questions regarding the role of aboveground biomass as a source of atmospheric H2 and mechanisms linking soil H2 and carbon cycling. Results from this study should be incorporated into modeling efforts to predict the response of the H2 soil sink to changes in anthropogenic H2 emissions and shifting soil conditions with climate and land-use change.