The uneven mapping of the Maltese continental shelf precludes a full assessment of its marine habitats, important for their monitoring and conservation in line with the EU Marine Strategy Framework Directive and local initiatives. From 2009 to 2012, high-resolution multibeam echosounder (MBES) surveys offshore the NW and E coasts of the Maltese archipelago were carried out, covering a total area of 1408.3 km(2) with a maximum resolution of 1 m, at depths from 1.5 to 263 m. The types of benthic habitats occurring on the continental shelf often showed subtle acoustic variations. This article aims at 1) integrating analyses of the bathymetry and acoustic textures with ground-truthing (grab samples) in key areas; 2) validating this combined approach by rewriting an existing benthic habitat map of the eastern continental shelf of Malta; 3) exploiting this ground-truthed classification to calibrate an unsupervised classification of a dataset acquired with a different sonar. The main results obtained from these analyses are i) a sediment map of the continental shelf of NW Malta and east of the Maltese archipelago - classifying in detail bedrock, rocky blocks, coarse sand and gravel, fine to medium sand and maerl, sand and gravel - that supports the geomorphological interpretation of the seabed features; ii) an automatic classification of the seafloor morphology, highlighting a very gentle sloping seabed crossed by the shelf break and by palaeo-river valleys; iii) the first full benthic habitat map of the continental shelf offshore E and NW coast of Malta obtained with a semi-automatic classification. In this work, we highlight and explain the main differences in seafloor sediment coverage, its morphology and the relative occurrences of benthic habitats between the NW and E sides of the Maltese archipelago. (C) 2017 Elsevier Ltd. All rights reserved.