Sulfur (S) and nitrogen (N) increasing anthropogenic emissions in the last century has arisen wide concern on the ecological effects of S and N deposition. In this paper, we use bulk deposition and stream water measurements in the central Pyrenees (PYR-C and PYR-AT sites) and Montseny (MSY-TM0) covering different time lengths in the period 1983–2017 to investigate how these mountain environments respond to ongoing changes of regional emissions to the atmosphere. PYR-C, in spite of its position far away from urban and industrial areas, presented higher SO4–S, NO3–N and NH4–N bulk deposition than the Montseny site closer to Barcelona and the inclusion of dry deposition only reversed this pattern for NO3–N. This indicates that distance to pollution sources does not protect these mountain sites from a considerable impact of pollution. Time-trends in SO4 2- and NO3 – concentrations in bulk deposition were similar between sites: SO4 2- monotonically decreased, while NO3 – increased until the mid-2000 s and decreased thereafter. In the period 1983 to 2017, SO2 emissions in Europe (EU-28) decreased by 95%, while in the SO4 2- concentrations in bulk deposition declined by 35–50% in Pyrenees and Montseny respectively and SO4 2- concentrations in the streams by 25–35%, respectively. Other sources of SO4 2- (e.g. episodic African dust) may explain the different reduction rate between anthropogenic emissions and bulk deposition. Net S budget was positive for MSY-TM0 (indicating flushing from the catchment) and negative for the PYR-C site (indicating retention), while it was close to zero for the other Pyrenean site, but in the PYR-C site net retention showed a significant increasing trend tending to lower retention in recent years. Bulk N deposition in the Pyrenees was lower but stream concentrations and export was higher than at Montseny, this leading to less N retention in the Pyrenean sites. However, the MSY-TM0 site showed a trend towards less N retention in recent years. This was driven by higher exports during the wet months, which would correspond to a first stage of N saturation according Stoddard’s classification.