Exploration of the marine environment using underwater remote-sensing methods is the most reasonable method for investigating submerged archaeological heritage sites, preserving their current condition and maintaining them for future generations. While non-invasive recognition of heritage sites is one of the main objectives of underwater archaeology, the nearshore environment of the small Polish town of Puck hides one of the biggest medieval harbours in the Baltic Sea. The following research objectives were met in this study: (a) exploration of underwater archaeological heritage harbour in Puck using high-resolution hydroacoustics, 3-D shallow seismics and underwater photogrammetry; (b) reconstruction of the submerged Puck medieval port by the combining of hydroacoustics, 3D shallow seismics, underwater photogrammetry and archival documentation; (c) estimation of the rate at which the bottom sediments containing the archaeological objects are being destroyed. The underwater archaeological site of Puck harbour was explored using multiple surveying methods, including multibeam echosounder, parametric sub-bottom profiler, underwater photogrammetry, aerial photography and comparison with archival documentation. Very highresolution bathymetry from a multibeam echosounder allowed seabed features suchas piles, stones and horizontal structural elements to be identified, along with other archaeological artefacts, boat wrecks and boat-building artefacts. The 3-D shallow seismic datasets allowed us to distinguish, for example, several outcropping structures, a previously unknown buried shipwreck, past excavation trenches, the harbour boundary and a palaeochannel of the Płutnica River. Fusing datasets from multiple sources in the geographic information system (GIS) environment allowed for a combined visualization of the heritage sites, providing a broad archaeological demonstration of the underwater structure. By comparing with archival documentation, we calculated that 43% of biogenic layers containing archaeological objects eroded over 26 years. Our results demonstrated that without any doubt, underwater remote-sensing methods are the most appropriate for exploration and investigation of underwater heritage sites while maintaining their original value.