Background <p>Determining the sources and contribution rates of metal contamination through multi-isotope analysis is an urgent and important topic in environmental research. However, acid digestion and extraction methods vary worldwide depending on the environmental media and researcher, potentially resulting in bias in measured concentrations and isotope ratios. Therefore, this study analyzed differences in element concentrations and multi-isotopic compositions (Cu, Zn, Pb, and Sr) between the total digestion and aqua regia extraction methods using six certified reference materials (CRMs) and 11 environmental samples.</p> Finding <p>Although differences depend on the type of CRM, the average recovery rates for metal elements extracted using the aqua regia extraction method ranged from 50.8% for Ti to 97.9% for Mn of the total concentration. For Cu, Zn, and Pb, which are widely used in environmental pollution research using stable isotopes, the average recovery rates obtained using the aqua regia extraction method were 97.5% for Cu, 97.6% for Zn, and 96.0% for Pb of the total contents, sufficiently high to warrant isotopic analysis. The Cu, Zn, and Pb isotopic compositions of CRMs did not differ between the two acid digestion methods and were consistent with previously reported results. For Sr, the average and range of recoveries extracted by the aqua regia extraction were 87.7% and 80.8–98.7%, respectively. The Sr isotopic composition in the aqua regia extraction was slightly lower than that in the total digestion method. However, considering the greater variability of strontium isotopes in environmental samples, the differences in Sr isotopic values across different acid digestion methods are likely to be minimal.</p> Conclusion <p>The concentration and isotopic composition of the CRMs using the aqua regia extraction method presented in this study will significantly contribute to improving the accuracy of analytical data for trace elements in environmental studies.</p>