In this work, the simultaneous determination of four organometallic species (monomethylmercury, monobutyltin, dibutyltin and tributyltin) in environmental samples by using a GC-MS system with electron ionisation has been established. The measurement of isotope ratios in each species was accomplished by selecting the most adequate molecular cluster, and simple mathematical equations were applied to correct the contributions of 13C from the organic groups attached to the tin and mercury atoms. The influence of different parameters such as dwell time on the precision and accuracy of the measured isotope ratios in each target species has also been studied. The determination and the sample preparation procedures presented in this work were first individually validated by analysing several certified reference materials for butyltin compounds (mussel tissue CRM-477 and marine sediment SOPH-1) and for monomethylmercury (tuna fish CRM-464) using an innovative focused microwave technology for the extraction of the species from the solid samples. Additionally, the simultaneous determination of the four species was successfully validated by obtaining quantitative recoveries in spiked natural waters and by analysing the certified reference material BCR-710 (certified in tributyltin and monomethylmercury). The values obtained in such certified tissue were fully in agreement not only with the certified mass fractions but also with the proposed indicative values for mono- and dibutyltin.