During the archaeological excavations in the Byzantine Theodosian harbor (Istanbul) a Holocene dark gray to black clay sequence was uncovered. This clay unit was deposited under anoxic conditions in a small swamp. Both wooden artifacts from the Neolithic period, but also dispersed organic matter were perfectly preserved within this sequence. The aim of this study was the assessment of environmental changes and anthropogenic impacts with the help of organic geochemical and isotopic characterization of organic matter in this clay unit. The age model, based on C-14 data, showed that the clay was deposited during a period about from 11,100 to 7500 cal. years BP. Hydrogen Index values lower than 100 mgHC/gTOC, n-alkane distributions with maxima at nC(29) or at nC(31), a predominance of long-chain n-alkanes (C-25-C-33) and delta C-13(org) values around -24 parts per thousand to -27 parts per thousand suggest a predominantly terrestrial origin of organic matter from C-3 plants. Obvious excursions of bulk delta C-13(org) and compound-specific delta C-13 and delta D values of nC(27), nC(29), nC(31), and nC(33) are interpreted as indicators of changes in environmental and climatic conditions. Several shifts toward colder and warmer climatic conditions were identified and dated. Furthermore, two sudden changes in the hydrological regime were dated to 9000-8820 cal. years BP and to 8150-8050 cal. years BP toward wetter and drier conditions, respectively. Specific molecular organic geochemical indicators such as faecal sterols or a strong enrichment of delta N-15 caused by human impact could not be detected. Therefore, the swamp should not have been intensively affected by Neolithic people and/or respective indicators of their influence have been diluted due to the high sedimentation rate.