Scour jeopardises the safety of many civil engineering structures with foundations in riverbeds and it is the leading cause for the collapse of bridges worldwide. Current approaches for bridge scour risk management rely mainly on visual inspections, which provide unreliable estimates of scour and of its effects, also considering the difficulties in visually monitoring the riverbed erosion around submerged foundations. Thus, there is a need to introduce systems capable of continuously monitoring the evolution of scour at bridge foundations, even during extreme flood events. This paper illustrates the development and deployment of a scour monitoring system consisting of smart probes equipped with electromagnetic sensors. This is the first application of this type of sensing probes to a real case-study for continuous scour monitoring. Designed to observe changes in the permittivity of the medium around bridge foundations, the sensors allow for detection of scour depths and the assessment of whether the scour hole has been refilled. The monitoring system was installed on the A76 200 Bridge in New Cumnock (S-W Scotland) and has provided a continuous recording of the scour for nearly two years. The scour data registered after a peak flood event (validated against actual measurements of scour during a bridge inspection) show the potential of the technology in providing continuous scour measures, even during extreme flood events, thus avoiding the deployment of divers for underwater examination.