This study presents an innovative approach to underwater archaeological prospection using non-invasive methods of seabed exploration. The research focuses on the Puck medieval harbour, a cultural heritage site, and utilises acoustic and optical underwater remote-sensing technology. The primary objectives include optimising the use of Airborne Laser Bathymetry in underwater archaeology, enhancing the filtration process for mapping underwater sites, and utilising data from both multibeam echosounder and bathymetric LiDAR for detailed archaeological research. A systematic approach to data processing is advocated to maximise the value of collected data and inform subsequent investigations. The study demonstrates the high accuracy of bathymetric datasets from optical and acoustic sources, with an R-squared correlation coefficient of 0.9853. The application of these techniques is demonstrated, underscoring the compatibility and effective combination of these methods in underwater archaeological exploration. This research provides valuable insights and directions for future archaeological prospections based on active remote-sensing measurements.