A methodology for automatically processing the data files from an EM3000 multibeam echosounder (Kongsberg Maritime, 300 kHz) is presented. Written in MatLab, it includes data extraction, bathymetry processing, computation of seafloor local slope, and a simple correction of the backscatter along-track banding effect. The success of the latter is dependent on operational restrictions, which are also detailed. This processing is applied to a dataset acquired in 2007 in the Tamaki Strait, New Zealand. The resulting maps are compared with a habitat classification obtained with the acoustic ground-discrimination software QTC View linked to a 200-kHz single-beam echosounder and to the imagery from a 100-kHz sidescan sonar survey, both performed in 2002. The multibeam backscatter map was found to be very similar to the sidescan imagery, quite correlated to the QTC View map on one site but mainly uncorrelated on another site. Hypotheses to explain these results are formulated and discussed. The maps and the comparison to prior surveys are used to draw conclusions on the quality of the code for further research on multibeam benthic habitat mapping.