The Neoria, or Venetian Dockyards, were built during the Venetian occupation of Crete (13th–17th centuries) to support shipbuilding and maintenance activities. These dockyards played a crucial role in the Republic of Venice's naval dominance in the Eastern Mediterranean. Characterised by their vaulted structures, the Neoria served as essential infrastructure for the city’s maritime economy, reflecting the strategic importance of Heraklion during the period. The high seismicity of Crete, combined with the deteriorating state of the historic dockyards, underscored the need for the structural assessment to inform preservation strategies and evaluate the long-term stability of the structures. This study presents how non-destructive testing techniques can enhance the accuracy of numerical modelling of historic structures, thereby supporting the development of effective restoration strategies. A 3D numerical model was developed to capture the complex geometry of the Neoria, including variations in masonry thickness, openings, boundary conditions and different materials. The model was calibrated using the results of a non-destructive testing campaign, which included sonic tests and ambient vibration dynamic identification tests. Nonlinear static pushover analyses simulated seismic loading, allowing for the evaluation of damage progression and potential failure mechanisms. The results underscored the importance of model calibration in predicting the seismic response of historic masonry, providing valuable insights to inform decisions on retrofitting the historic structure.