Inspections of engineered structures below water level are essential to ensure the long-term serviceability of bridge infrastructure and to avoid major damage or failure. This research aimed to investigate integrated geophysical technologies for the underwater inspection of bridge foundation-related scour and erodible scour-based infill. Survey methods focused on Water-Penetrating Radar (WPR), supplemented by sonar. Whilst the survey benefits of the sonar imaging water–sediment interface and structures are well known, those of WPR are not. However, it is ideally suited to the survey of the water base and sub-sediment in shallow (>10 m) freshwater, especially where suspended sediment, weed infestation or methane impede sonar results. Our work produced good WPR imagery acquired from small, manoeuvrable boats that allowed bathymetric profiles to be plotted, as well as the likely locations of soft-sediment scour in future high-water flow events. This study provides clear benefits for integrated sonar and WPR surveys in the quantitative assessment of engineered structures within freshwater.