Leaching of macronutrients such as nitrogen, phosphorus and potassium from soils is of particular interest in the Baltic Sea region because of its adverse effects on water quality. The objective of this study was to evaluate macronutrient leaching in a juvenile hybrid aspen (Populus tremula L. × P. tremuloides Michx.) plantation cultivated in an agroforestry system and fertilized with biogas production residues, wastewater sludge and wood ash in hemi-boreal climate conditions. Analysis of macronutrient concentrations in the soil solution showed that annual macronutrient leaching decreased over time after the establishment of the plantation and application of fertilizers. Moreover, macronutrient leaching was affected not only by meteorological conditions, but also by the type of fertilizer used. During the five years after establishment of the plantation, nitrate-nitrogen leaching decreased up to 99.6%, phosphate-phosphorus leaching decreased up to 97.1%, but potassium ions leaching decreased up to 76.5%. Nevertheless, juvenile hybrid aspen plantations cultivated in an agroforestry system remain an important part in mitigation of leaching of macronutrients from agricultural lands in the Baltic Sea region.