AbstractThree‐dimensional (3D) models derived from digital survey techniques have increasingly become a mainstay of archaeological research and cultural heritage management. The high accuracy of such modelling makes it an attractive solution for a wide range of challenges from site recording and interpretation to object analysis and reconstruction. The present paper focuses on a new 3D digitization method using stereoscopic video for the documentation, analysis, and representation of archaeological contexts as part of shipwreck investigations off southeast Sicily at Marzamemi. This sixth‐century ce vessel sank in shallow water (7–8 m) while carrying a massive cargo of largely prefabricated architectural elements intended for the construction and decoration of a church somewhere in the late antique west. This dynamic site presents significant challenges to the interpretation of depositional and post‐depositional events as well the reconstruction of the original cargo and individual architectural elements. Therefore, 3D documentation underwater at Marzamemi has centred on new methods for stereoscopic scanning of the site, topography, and large architectural finds, allowing not only more rapid and precise mapping but insights into site formation processes and the organizational mechanisms behind the cargo assemblage. The adoption of this new system based on a precise workflow and simple, inexpensive hardware combined with readily available software allows more accurate and rapid digital recording underwater to a high standard across scales, from the site level down to the individual artefact. This process, named ISU3D (Integrated System for Underwater 3D Digitization), offers innovative solutions not only for archaeological field research but for heritage management and public outreach.