Monitoring of water quality is important to control water pollution. Contamination of the aquatic system has a large effect on human health and the environment. Under the European Water Framework Directive (WFD) 2000/60/EC and the related directive on environmental quality standards (EQS) in the field of water policy 2008/105/EC, the need for sensitive reference methods was highlighted. Since tributyltin (TBT) is one of the WFD listed priority substances a method was developed which is capable to qualify and quantify the pollutant at the required low WFD EQS of 0.2 ng L-1 in whole water bodies, i.e. in non-filtered water samples with dissolved organic carbon and suspended particulate matter. Therefore special attention was paid on the interaction of TBT with the suspended particulate matter and humic substances to obtain a complete representation of the pollution in surface waters. Different water samples were investigated varying the content of organic dissolved and suspended matter. Quantification was performed using species-specific isotope dilution (SSID) and gas chromatography with inductively coupled plasma mass spectrometry (GC-ICP-MS). Different sample treatment strategies were evaluated and compared. The process of internal standard addition was investigated and optimized, hence the equilibrium between internal standards and matrix is of primary importance to perform accurate SSID. Samples spiked at EQS level were analyzed with a recovery between 95 and 105 %. Additionally real surface water samples were investigated and the TBT concentration for the whole water body was determined and compared with conventional routine analysis method. (C) 2016 Elsevier B.V. All rights reserved.