Short-wavelength, low-amplitude magnetic anomalies form dendritic patterns on the shallow water (<100 m depth) Magdalen Plateau in the Gulf of St Lawrence, Canada. High-resolution seismic data indicate that these magnetic anomalies are associated with 0.6–2 km wide incised Quaternary valleys with relatively flat bottoms lying 30–70 m below the seafloor. The magnetic signature of the valleys is due to high magnetic susceptibility volcanic detritus derived from the erosion of the volcanic rocks that overlie most of the salt bodies in this area. This study shows that magnetic data may be a useful tool for mapping surficial sediments. These magnetic data provide the first offshore evidence for the direction of major water discharge. It remains unclear whether the valleys were formed by river incision during one or several regional lowstand(s) or from one or several sub-glacial discharge episode(s) across the Magdalen Plateau. The valley evidence should be incorporated into any future palaeogeographical reconstructions.