A Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) extraction method combined with Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) for determination of organotin compounds (OTC) has been newly developed. The novel analytical method was validated and the quality of the results was tested by the use of certificate reference material of freshwater sediment BCR 646. The method was applied in determination of OTC concentration in real samples of bottom sediments collected from the Polish part of Odra River Estuary. The samples came from locations with different anthropogenic impact. Additionally, the extraction recovery of OTC and matrix effect on MS signal response was investigated based on those real environmental samples. It was found that organic compounds and anthropogenic contaminations present in bottom sediments may affect extraction efficiency of the organotin compounds (OTC) and change the matrix effect on MS signal response. The highest concentrations of tributyltin were found in bottom sediments collected from locations in vicinity of the Szczecin harbor and shipyards. The presence of triphenyltin above limit of detection (5 ng TPhT/g of sediment) was observed only in two samples and its concentration was several times lower compared to concentration of tributyltin (from 58 ng/g to 5263 ng/g). In spite of the fact that, the application of TBT-based paints on hull of vessel entering EU ports has been banned by European Commission regulation No. 782/2003 since 2008, the OTC compounds are still present in bottom sediment and pose significant threat to the environment. This threat should be taken into account during dredging of waterways and other hydrotechnical works.