A sensitive and accurate method is developed for the simultaneous ultra-trace determination of tributyltin (TBT), dibutyltin (DBT), monobutyltin (MBT), methylmercury (MeHg) and inorganic mercury (iHg) in waters including seawater by dynamic headspace in-tube extraction (dHS-ITEX) and GC-ICPMS detection. Quantitation of TBT, DBT, iHg and MeHg was achieved by isotope dilution mass spectrometry using 117Sn-enriched TBT and DBT, 201Hg-enriched iHg and enriched Me198Hg (NRC CRM EMMS-1), respectively, wherein analyte mass fractions in enriched spikes were determined by reverse isotope dilution at the same time using natural abundance TBT, DBT, iHg and MeHg primary standards by exactly matching the analyte and enriched spikes. Quantitation of MBT was realized by standard addition calibration with 117Sn-enriched DBT serving as the internal standard. The proposed method achieved detection limits of 0.06, 0.08 and 1.1 pg g−1 (as Sn) for TBT, DBT and MBT and 0.08 and 0.4 pg g−1 (as Hg) for MeHg and iHg, respectively. Validation of the proposed method was demonstrated by quantitative spike recoveries of 94–105% at 5 to 50 pg g−1 levels achieved in drinking water, river water and seawater, demonstrating the accuracy of the method. The obtained detection limits are sufficiently low to perform measurements in support of the Water Framework Directive. The developed method was applied for the determination of butyltins, iHg and MeHg in drinking water (AQUA-1), river water (SLRS-6) and seawater (CASS-6 and NASS-7) samples. Values of 0.124 ± 0.041 and 0.157 ± 0.060 pg g−1 (1SD, n = 4) for MeHg in CASS-6 and NASS-7 and values of 1.74 ± 0.61, 22.15 ± 0.13, and 31.42 ± 0.30 pg g−1 (1SD, n = 4) for iHg in SLRS-6, CASS-6 and NASS-7 were obtained, respectively. A value of 2.27 ± 0.45 pg g−1 as Sn for MBT was detected in NASS-7 seawater, whereas other butyltins were below the detection limits in the waters.