Future increase of atmospheric nitrogen deposition in tropical regions is expected to have negative impacts on forests ecosystems and related biogeochemical processes. In tropical mountain forests topography causes complex streamflow and rainfall patterns, governing the atmospheric transport of pollutants and the intensity and spatial variability of deposition. The main goal of the current study is to link spatio-temporal patterns of upwind nitrogen emissions and nitrate deposition in the San Francisco Valley (eastern Andes of southern Ecuador) at different altitudinal levels. The work is based on Scanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY) retrieved-NO2 concentrations, NOx biomass burning emissions from the Global Fire Emissions Database (GFEDv3), and regional vehicle emissions inventory (SA-INV) for urban emissions in South America. The emission data is used as input for lagrangian atmospheric backward trajectory modeling (FLEXTRA) to model the transport to the study area. The results show that NO3?NO3? concentrations in occult precipitation samples are significantly correlated to long-range atmospheric secondary nitrogen transport at the highest meteorological stations (MSs) only, whereas for NO3?NO3? concentrations in rain samples this correlation is more pronounced at the lower MSs. We conclude that ion concentrations in occult precipitation at the uppermost MSs are mainly linked to distant emission sources via the synoptic circulation impinging the more exposed higher sites. Lower correlations close to the valley bottom are due to a lower occult precipitation frequency and point to a contamination of the samples by local pollution sources not captured by the used emission data sources.