The current research paper presents the results of the first regional assessment of sediment contamination by dioxins (polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (dl-PCBs)) in the south-eastern part of the Baltic Sea (Lithuanian and Polish marine areas) during the periods of 2014 and 2019–2020. In total, 143 surface and core sediment samples were taken of existing offshore dredged-soil-disposal sites in the area of the former shipyard in the Port of Gdynia (Poland), as well as in a profile from the nearshore to the deeps of the Gdansk basin, following the natural pattern of sediment migration in the region. The obtained results indicated wide variation in both the total content of the investigated compounds as well as the profiles of congeners, indicating the likely sources of their origin. Based on the obtained concentration characteristic profiles of the congeners, we determined the amount of dioxins and the likely sources of their origin in the Gdansk Basin. The profiles showed elevated contents of octa- and hepta-chlorodibenzodioxins (OCDD and HpCDD) in the sediments, while the fractions of most other toxic congeners were considerably lower. The domination of OCDF in the spectrum of the studied PCDFs suggests the possible contribution of industrial processes. The obtained results have filled the gaps in our knowledge while providing a perfect background for more detailed discussions concerning the accumulation of dioxins in surface sediments from the south-eastern part of the Baltic Sea.