Invaluable historical heritage needs peculiar protections from natural hazards. Seismic risk is one of the most dangerous menaces for historical building, due to their critical seismic response. Venice historical center and its lagoon (Italy) is one of the most famous humanity assets. The city center is an urban complex grown in more than one thousand years, based on poor lagoon sediments. This urban environment is particularly fragile. From a technical point of view it presents several limitations to characterize subsoil properties, especially seismic velocities of soil. In this study it is proposed the single station frequency-time analysis (FTAN) as efficient shear wave velocity survey methodology. FTAN procedure has very simplified field logistics, if compared to multi-channels common methods. The work presents a case study of FTAN applications on several sites of the Venice historical center and its lagoon. The application of this geophysical technique allows an estimation of the seismic velocities of soil, necessary for seismic response evaluations. Thanks to the results of shear-wave velocity the soil was classified by the use of the seismic European classification and the Italian earthquake-proof regulation. Since the Venice subsoil is characterized from inhomogeneous deposits, even very near sites can present different seismic velocities. The work results enhance these different soil properties, in good agreement with the most recent lithostratigraphic reconstruction of the Venice subsoil. Different Vs conditions can lead to substantially different seismic behaviors, imposing particular characterizations for aseismic purposes and site response analyses. FTAN methodology efficiently meets geological reconstruction. This non invasive procedure seems to accurately answer the modern anti-seismic design requirements, even in such a difficult historical urban complex.