The Three Gorges Project is the largest hydro project in the world, and the water level of the Three Gorges Reservoir (TGR) is dynamic and adjustable with the aim of flood control and electrical power generation. It is necessary to investigate the pollutants and their underlying contamination processes under dynamic water levels to determine their environmental behaviors in the Three Gorges Reservoir Area (TGRA). Here, we report the assessment of organotin compounds (OTs) pollution in the river sediments of the TGRA. Surface sediment samples were collected in the TGRA at low and high water levels. Tributyltin (TBT), triphenyltin (TPhT), and their degradation products in sediments were quantified by gas chromatography-mass spectrometry. Butyltins (BTs) and phenyltins (PhTs) were detected in sediments, and BTs predominated over PhTs in the whole study area under dynamic water level conditions. The concentrations of OTs in sediments varied markedly among locations, and significant concentrations were found in river areas with high levels of boat traffic and wastewater discharge. Sediments at all stations except Cuntan were lightly contaminated with TBT, and total organic carbon (TOC) was a significant factor affecting the fate of TBT in the TGRA. The butyltin and phenyltin degradation indices showed no recent inputs of TBT or TPhT into this region, with the exception of fresh TPhT input at Xiakou Town. Shipping activity, wastewater discharge, and agriculture are the most likely sources of OTs in the TGRA.