The establishment of multibeam echosounders (MBES), as a mainstream tool in ocean mapping, has facilitated integrative approaches towards nautical charting, benthic habitat mapping, and seafloor geotechnical surveys. The combined acoustic response of the seabed and the subsurface can vary with MBES operating frequency. At worst, this can make for difficulties in merging the results from different mapping systems or mapping campaigns. However, at best, having observations of the same seafloor at different acoustic wavelengths allows for increased discriminatory power in seabed classification and characterization efforts. Here, we present the results from trials of a multispectral multibeam system (R2Sonic 2026 MBES, manufactured by R2Sonic, LLC, Austin, TX, USA) in the Bedford Basin, Nova Scotia. In this system, the frequency can be modified on a ping-by-ping basis, which can provide multi-spectral acoustic measurements with a single pass of the survey platform. The surveys were conducted at three operating frequencies (100, 200, and 400 kHz), and the resulting backscatter mosaics revealed differences in parts of the survey area between the frequencies. Ground validation surveys using a combination of underwater video transects and benthic grab and core sampling confirmed that these differences were due to coarse, dredge spoil material underlying a surface cover of mud. These innovations offer tremendous potential for application in the area of seafloor geological and benthic habitat mapping.