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Marine magnetic surveys have traditionally been performed towing scalar magnetometers behind the vessel. We have investigated the possibility of replacing them by shipborne vector magnetometers. For this purpose, we have acquired two surveys in the shallow waters of the Bay of Brest and the Iroise Sea (NE Atlantic). Coincident shipborne vector and towed-scalar magnetometers have been deployed from two carriers: at the prow of the 8 m-long launch VH Goéland and on the mast of the 59 m-long hydrographic vessel BH2 Laplace. The shipborne vector sensor is significantly affected by noise related to the ship’s remanent and induced magnetisations than can reach thousands of nanoteslas (nT). We have mitigated these effects by acquiring figures of merit and computing compensation factors that removed over 95% of this noise. After low-pass filtering and offset corrections, we found that the resulting magnetic anomaly maps are fairly close to those obtained with the coincident towed-scalar data. We have resolved anomalies as small as 10 nT related to anthropogenic metal objects and 20 nT related to geological features interpreted as dolerite dikes. These results confirm that shipborne vector magnetometers could be a valid alternative to towed-scalar systems, especially in coastal shallow and busy waters.