During the salvage excavations in the area of the former Theodosian harbor in Yenikapi-Istanbul several ship wrecks from the Byzantine period, archaeological objects from different periods and a Holocene aged sedimentary sequence have been uncovered. In this study the lithological, lithostratigraphical and facies properties of the Holocene sequence are investigated in detail and its depositional environment is determined. For this purpose along four profiles (S1, S2, S3, S4) 14 different sections of a total thickness of 17.75 m are studied and 100 samples are collected. The grain size distribution and mineralogical composition of the samples are defined by sieve and sedigraph analysis and by XRD method, respectively. Results of these analyses and facies characteristics of this poorly known Holocene sequence are used for the definition of the depositional environment. Accordingly, the marine sediments are deposited in a near-shore environment, with a natural embayment or estuary transgressively. Terrigenous and anthropogenic material carried by the Lycos River, at the mouth of this natural embayment, resulted in first a regression and then a high-energy fluvial system in the study area.