We use various geophysical datasets (multibeam and singlebeam echosounder data, sub-bottom profiling Chirp and sonar data and very high-resolution boomer seismic data) along with published sedimentological data and depth data from nautical charts in order to create models of the depth of the seafloor and the base of Holocene marine sediment in the Gulf of Trieste. The two models are later used in order to calculate the thickness of marine Holocene sediment which has been depositing on the Late Pleistocene alluvial plain since the Holocene transgression in the Italian and Slovenian parts of the gulf. Thicker Holocene marine sedimentary sequences averaging at around 5 m are characteristic for the southeastern part of the gulf. In other parts of the gulf the Holocene marine sedimentary cover is very thin or even absent, except in close proximity to the shoreline and fluvial sediment sources, in the area of the Trezza Grande paleodelta and above topographic depressions of the Late Pleistocene base. The presented datasets available from the OGS SNAP data repository (http://doi.org/cpz2) represent a valuable reference for a wide variety of research disciplines dealing with the dynamic Earth system in the Gulf of Trieste and could be used as a valuable tool for designing sampling and geophysical campaigns in the studied area.