Serum calcium (Ca), bone biomarkers, and radiological imaging do not allow accurate evaluation of bone mineral balance (BMB), a key determinant of bone mineral density (BMD) and fracture risk. We studied naturally occurring stable (non‐radioactive) Ca isotopes in different body pools as a potential biomarker of BMB. ⁴²Ca and ⁴⁴Ca are absorbed from our diet and sequestered into different body compartments following kinetic principles of isotope fractionation;​ isotopically light ⁴²Ca is preferentially incorporated into bone, whereas heavier ⁴⁴Ca preferentially remains in blood and is excreted in urine and feces. Their ratio (δ^44/42Ca) in serum and urine increases during bone formation and decreases with bone resorption. In 117 healthy participants, we measured Ca isotopes, biomarkers, and BMD by dual‐energy X‐ray absorptiometry (DXA) and tibial peripheral quantitative CT (pQCT). ⁴⁴Ca and ⁴²Ca were measured by multi‐collector ionization‐coupled plasma mass‐spectrometry in serum, urine, and feces. The relationship between bone Ca gain and loss was calculated using a compartment model. δ^44/42Ca_serum and δ^44/42Ca_urine were higher in children (n = 66, median age 13 years) compared with adults (n = 51, median age 28 years;​ p < 0.0001 and p = 0.008, respectively). δ^44/42Ca_serum increased with height in boys (p < 0.001, R² = 0.65) and was greatest at Tanner stage 4. δ^44/42Ca_serum correlated positively with biomarkers of bone formation (25‐hydroxyvitaminD [p < 0.0001, R² = 0.37] and alkaline phosphatase [p = 0.009, R² = 0.18]) and negatively with bone resorption marker parathyroid hormone (PTH;​ p = 0.03, R² = 0.13). δ^44/42Ca_serum strongly positively correlated with tibial cortical BMD Z‐score (n = 62;​ p < 0.001, R² = 0.39) but not DXA. Independent predictors of tibial cortical BMD Z‐score were δ^44/42Ca_serum (p = 0.004, β = 0.37), 25‐hydroxyvitaminD (p = 0.04, β = 0.19) and PTH (p = 0.03, β = −0.13), together predicting 76% of variability. In conclusion, naturally occurring Ca isotope ratios in different body compartments may provide a novel, non‐invasive method of assessing bone mineralization. Defining an accurate biomarker of BMB could form the basis of future studies investigating Ca dynamics in disease states and the impact of treatments that affect bone homeostasis.