The knowledge of the evolution of the scour around a vertical cylinder placed in a sandy bed and exposed to waves is of fundamental importance in oceanic engineering. Measurements of this phenomenon are very difficult to be performed due to the mandatory constraint of adopting non-invasive techniques. In this paper a novel three-dimensional measurement technique which uses a stereo vision approach has been adopted in order to dynamically recover the bottom characteristics. In particular, the sandy bottom time evolution was here observed from the flat bed initial condition until a stable configuration was attained. Moreover some morphological parameters of the scour such as the maximum scour depth, the extension of the eroded area and the position of the maximum scour toe were measured at equilibrium condition. These quantities were estimated with an average relative accuracy of about 5%, which appears particularly appropriate if compared to the results given by traditional measurement strategies. These latter being not particularly suitable for dynamic analysis of bottom evolution. The experimental investigation performed in this paper allowed to confirm some theoretical hypotheses, such as that of considering the Keulegan–Carpenter number (KC) as the key parameter which controls the phenomenon, to be confirmed. Moreover the experimental measures of the scour depth at equilibrium stage, has been compared with the values given by the relation proposed by Sumer et al. (1992) giving a fairly good agreement. Finally, with regards to other three-dimensional features such as the eroded area, new relations with standard dimensionless parameters have been proposed that result useful for design purposes.