Nutrient imbalances may negatively affect the health status of forests exposed to multiple stress factors, including drought and bark beetle calamities. We studied the origin of base cations in runoff from a small Carpathian catchment underlain by base-poor flysch turbidites using magnesium (Mg), calcium (Ca) and strontium (Sr) isotope composition of 10 ecosystem compartments. Our objective was to constrain conclusions drawn from long-term hydrochemical monitoring of inputs and outputs. Annual export of Mg, Ca and Sr exceeds 5-to-15 times their atmospheric input. Mass budgets per se thus indicate sizeable net leaching of Mg, Ca and Sr from bedrock sandstones and claystones. Surprisingly, δ26Mg, δ44Ca and 87Sr/86Sr isotope ratios of runoff were practically identical to those of atmospheric deposition and soil water but significantly different from bedrock isotope ratios. We did not find any carbonates in the studied area as a hypothetical, easily dissolvable source of base cations whose isotope composition might corroborate the predominance of geogenic base cations in the runoff. Marine carbonates typically have lower δ26Mg and 87Sr/86Sr ratios, and silicate sediments often have higher δ26Mg and 87Sr/86Sr ratios than runoff at the study site. Mixing of these two sources, if confirmed, could reconcile the flux and isotope data.