The structural deformation monitoring of civil infrastructures can be performed using different geomatic techniques: topographic measurements with total stations and levels, TLS (terrestrial laser scanning) acquisitions, and drone-based SfM (structure from motion) photogrammetric surveys, among others, can be applied. In this work, these techniques are used for the floodgate gaps and the rubber joints deformation monitoring of the MOSE system (Modulo Sperimentale Elettromeccanico), the civil infrastructure that protects Venice and its lagoon (Italy) from high waters. Since the floodgates are submerged most of the time and cannot be directly measured and monitored using high-precision data, topographic surveys were performed in accessible underwater tunnels. In this way, after the calculation of the coordinates of some reference points, the coordinates of the floodgate corners were estimated knowing the geometric characteristics of the system. A specific activity required the acquisition of the TLS scans of the stairwells in the shoulder structures of the Treporti barrier because many of the reference points fixed on the structures were lost during the placement of elements on the seabed. They were replaced with new points whose coordinates in the project/as-built reference system were calculated by applying the Procrustean algorithm by means of homologous points. The procedure allowed the estimation of the transformation parameters with maximum residuals of less than 2.5 cm, a value in agreement with the approximation of the real concrete structures built. Using the obtained parameters, the coordinates of the new reference points were calculated in the project reference system. Once the 3D orientation of all caissons in the barrier was reconstructed, the widths of the floodgate gaps were estimated and compared with the designed values and over time. The obtained values were validated in the Treporti barrier using a drone-based SfM photogrammetric survey of the eight raised floodgates, starting from the east shoulder caisson. The comparison between floodgate gaps estimated from topographic and TLS surveys, and those obtained from measurements on the 3D photogrammetric model, provided a maximum difference of 1.6 cm.