We developed a fully automated magnetic field scanner dedicated to uniaxial magnetic field measurements to determine remanent magnetization intensities and their variations in sedimentary U-channels. A fluxgate magnetometer located as close as possible to the sedimentary section is used to perform uniaxial measurements of magnetic fields generated by the isothermal remanent magnetization of the sediment. This artificial magnetization, which is known to be a powerful proxy in environmental magnetism, is produced perpendicular to the U-channel long axis, and parallel to the fluxgate axis, using a Halbach cylinder prior to the measurement. The present magnetic scanner offers a maximal spatial resolution of 5.8 mm for point sources. A spatial resolution of 14 mm is obtained for U-channel samples. The magnetic scanner presents a reliable magnetic field range over about 3 orders of magnitude allowing measurement of magnetizations that saturate the Superconducting Rock Magnetometer in its classical configuration. The estimation of remanent magnetization intensities along the U-channel is based on a modeling approach that uses successive uniformly magnetized prisms. In lacustrine laminated sections, comparison between modeling results based on prisms of a constant thickness, on prisms determined from sedimentary facies, and on prisms determined from X-ray fluorescence data helps to understand the detrital versus diagenetic history of the sedimentary succession.