This study examines the role of tree canopies in processing atmospheric nitrogen (Ndep) for four forests in the United Kingdom subjected to different Ndep: Scots pine and beech stands under high Ndep (HN, 13–19 kg N ha−1 yr−1), compared to Scots pine and beech stands under low Ndep (LN, 9 kg N ha−1 yr−1). Changes of NO3-N and NH4-N concentrations in rainfall (RF) and throughfall (TF) together with a quadruple isotope approach, which combines δ18O, Δ17O and δ15N in NO3− and δ15N in NH4+, were used to assess N transformations by the canopies. Generally, HN sites showed higher NH4-N and NO3-N concentrations in RF compared to the LN sites. Similar values of δ15N-NO3− and δ18O in RF suggested similar source of atmospheric NO3− (i.e. local traffic), while more positive values for δ15N-NH4+ at HN compared to LN likely reflected the contribution of dry NHx deposition from intensive local farming. The isotopic signatures of the N-forms changed after interacting with tree canopies. Indeed, 15N-enriched NH4+ in TF compared to RF at all sites suggested that canopies played an important role in buffering dry Ndep also at the low Ndep site. Using two independent methods, based on δ18O and Δ17O, we quantified for the first time the proportion of NO3− in TF, which derived from nitrification occurring in tree canopies at the HN site. Specifically, for Scots pine, all the considered isotope approaches detected biological nitrification. By contrast for the beech, only using the mixing model with Δ17O, we were able to depict the occurrence of nitrification within canopies. Our study suggests that tree canopies play an active role in the N cycling within forest ecosystems. Processing of Ndep within canopies should not be neglected and needs further exploration, with the combination of multiple isotope tracers, with particular reference to Δ17O.