Analytical methods for speciation of targeted organotin compounds (TBT and TPT) in water samples using SPE cartridge and liquid-liquid extraction has been carried out. Also, sediment analysis using methanolacid digestion and acid-sonication extraction methods also were developed. Different parameters affecting extraction and peak resolution were optimized. Also, three derivatization procedures were optimized. The accuracy of the extraction procedure also was verified on certified reference material (BCR-462) certified for TBT (54±15 μg/kg) and DBT (68±12 μg/kg). Freeze-dried mussel tissue (ERM-CE 477) was certified for TBT (2.20±0.19 mg/kg), DBT (1.54±0.12 mg/kg), and MBT (1.50±0.28 mg/kg). The two certified reference materials were used for recovery experiments. Good recoveries were obtained with methanol-acid digestion. The result was validated by analyzing the real water and sediment samples collected from Cape Town harbor and the compounds were detected in both water and sediment samples. Extraction of water samples with SPE gave better recovery for TPT than TBT. Performance characteristics such as linearity, detection limit (LOD), quantification limit (LOQ), and recovery were determined. Recoveries of TBT and TPT in spiked water using SPE were 65% and 70%, respectively. Quantitative recoveries also were recorded for the certified reference standards of sediments and mussel materials used.