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Ecohydrological and biogeochemical processes in tropical montane forests canopies are key in the provision of water‐related ecosystem services. However, the sustainability of these services is threatened by environmental change. Climate change in the tropics is suggested to be characterized by an increase in hydrological extremes, with El Niño Southern Oscillations (ENSO) as the main mechanism of climatic variability. For 2 years, we studied the effects of climate variability on a seasonal scale (represented by two phases of the ENSO) on nutrient exchange between rain and the canopy of two types of forests in the central Andes of Colombia. We monitored weekly precipitation, throughfall, and stemflow, and monthly samples of each were taken for nutrient determination in the laboratory. Our results show that forest canopies generally produced nutrient concentration enrichment in throughfall and stemflow, in both wet and dry seasons, with higher values in the Neutral period than in the El Niño period. The two phases of the ENSO did not significantly affect nutrient fluxes through the canopy. In the long term, with interannual climatic variations (seasonality and ENSO phases), the physical, chemical, and biological processes associated with the dynamics of nutrient exchange between rainwater and the canopy can alter the nutrient cycling in the forest. Our results suggest that changes in meteorological conditions such as the increase and intensification of droughts, and increases in the transformation of natural forests, could affect the capacity to regulate functions of tropical montane forests, threatening the provision of ecosystem services associated with water and soil.