Bottom structure of the basins in the Port of Gdynia, Poland, was analysed based on the archival materials of the Department of Operational Oceanography of Marine Institute in Gdańsk, particularly seismic profiles and macroscopic descriptions of sediment cores. Seismic profiling and core collection were performed in selected basins and within the fairway. The rich source material was used to draw a detailed bathymetric map of the bottom of the basins, a map of surface sediments, and a synthetic geological cross-section. A considerable variation in bottom depth within the analysed basins was observed. Bedrock sediments comprised Miocene sands and silts covered with glacial and fluvioglacial sediments, which reach the surface of the water, especially in the central part of the fairway. Within the eastern part of the fairway, fluvioglacial sediments are covered with marine sediments related to the Littorina transgression. Within the inner port and in the outport, a series of glacial and fluvioglacial sediments are covered with a thick (about 10 m) series of glaciolacustrine and lacustrine sediments, which in turn is covered with fluvial and deltaic sediments. The surface of the bottom is composed of contemporary, anthropogenically modified sediments. The map of surface sediments of the bottom corresponds to the geological map on the horizon of about 10 meters beneath land surface.