This paper presents an analysis of the recent tropospheric molecular hydrogen (H<sub>2</sub>) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H<sub>2</sub> surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N<sub>2</sub> fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H<sub>2</sub> budget. The net H<sub>2</sub> flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr<sup>−1</sup>. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H<sub>2</sub> soil uptake is −59±9 Tg yr<sup>−1</sup>. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H<sub>2</sub> emissions estimated using a H<sub>2</sub>/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H<sub>2</sub> sources and sinks.