The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC∕dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO−3 leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from −70 to 826 g C m−2 yr−1 at total wet + dry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 g N m−2 yr−1 and from −4 to 361 g C m−2 yr−1 at Ndep rates of 0.1 to 3.1 g N m−2 yr−1 in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated Ndep where Nr leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO−3 were on average 27 % (range 6 %–54 %) of Ndep at sites with Ndep < 1 g N m−2 yr−1 versus 65 % (range 35 %–85 %) for Ndep > 3 g N m−2 yr−1. Such large levels of Nr loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with Nr deposition up to 2–2.5 g N m−2 yr−1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP ∕ GPP ratio). At elevated Ndep levels (> 2.5 g N m−2 yr−1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC∕dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.