Knowledge of the origin of magnesium (Mg) and calcium (Ca) in soil solutions and catchment runoff helps to predict forest ecosystems’ vulnerability to deficiencies in essential nutrients in an era of climate change, environmental pollution and bark-beetle calamities. Here we discuss isotope aspects of Mg, Ca and strontium (Sr) cycling in a spruce-forested headwater catchment in a relatively unpolluted part of Central Europe. We investigated to what extent Mg and Ca isotope signatures of runoff reflect the isotope compositions of specific Mg- and Ca-rich minerals that easily dissolve during the weathering of paragneiss, and compared the isotope variability of Mg and Ca in fresh bedrock minerals, soils and other ecosystem reservoirs. We also compared conclusions from Mg and Ca isotope systematics with inferences from catchment input–output mass budgets. Long-term input–output monitoring in the studied catchment situated near the Czech–German border (Central Europe) revealed 3.5–7 times higher outputs of Mg, Ca, and Sr via surface runoff relative to their present-day atmospheric inputs. It follows that hydrological exports of recent atmospheric Mg, Ca and Sr are minor. Release of geogenic base cations into the runoff results from the interplay between mineral abundances, concentrations of the studied elements in the minerals, and their dissolution rates. Chemical depletion fractions for the studied elements from bedrock to the soil were 50–70 %, and the losses of dominant soluble minerals in the soil were 30–80 %. Exports of residual Mg, Ca and Sr following partial incorporation of these elements into secondary phyllosilicates are probably low because newly-formed clay minerals are not abundant in the soil. Residual Ca following preferential incorporation of isotopically light Ca into growing tree biomass may contribute to the isotopically heavy runoff Ca. Isotope ratios of base cations were obtained for six minerals (plagioclase, orthoclase, biotite, muscovite, apatite, and ilmenite). Mineral fractions differ greatly in δ²⁶Mg and δ⁴⁴Ca values and ⁸⁷Sr/⁸⁶Sr ratios. 80–97 % of each of the three studied base cations are present in the bedrock in a single relatively easily dissolvable mineral: Mg in biotite, and Ca and Sr in plagioclase. The isotope composition of Mg in biotite was similar to the isotope composition of Mg in runoff. The isotope compositions of Ca and Sr in plagioclase were also similar to Ca and Sr isotope compositions in runoff. Thus, the dominant geogenic source of each of the studied elements (Mg, Ca and Sr) in the investigated paragneiss catchment can be represented by one relatively soluble mineral.