Spatial surveys of marine benthic habitats and biota based on the interpretation of acoustic data were carried out at two sites in the eastern English Channel each representing different scales of geographic area and intensity of survey. A small area (4×12 km) crossing the Hastings Shingle Bank was surveyed at a relatively high intensity (track spacing 400 m) and was nested within a larger area between Hastings and Dungeness (12×40 km), which was surveyed at a lower intensity (track spacing 2 km). Surveys were conducted with two acoustic ground discrimination systems (AGDS), RoxAnn and QTC-VIEW and the primary purpose of the investigation was to compare the performance of the two AGDS using a common approach to analysis of the different data outputs (E1 and E2 for RoxAnn and the Q eigenvectors from QTC-VIEW). Exploratory data analysis using variography indicated that interpolation between tracks was justified for the smaller site to create a complete coverage, but was limited to the creation of a digital image of the track data for the larger area. Grab and video sample data were available for supervised classification of the AGDS data and interpreted sidescan images for comparison with unsupervised classification. Both AGDS gave similar outputs, although RoxAnn consistently gave slightly better levels of performance than QTC-VIEW as measured using error matrices. Although the investigation was not designed to compare the performance of AGDS and sidescan, the outputs from AGDS were similar to the visual interpretation of the sidescan sonar data. It was concluded that despite the inherent limitations of AGDS, they may be suitable for providing distribution maps at a broad scale that can give a context for the interpretation of finer scale survey of smaller, nested areas.