Acoustic methods are routinely used to provide broad scale information on the geographical distribution of benthic marine habitats and sedimentary environments. Although single-frequency multibeam echosounder surveys have dominated seabed characterisation for decades, multifrequency approaches are now gaining favour in order to capture different frequency responses from the same seabed type. The aim of this study is to develop a robust modelling framework for testing the potential application and value of multifrequency (30, 95, and 300 kHz) multibeam backscatter responses to characterize sediments’ grain size in an area with strong geomorphological gradients and benthic ecological variability. We fit a generalized linear model on a multibeam backscatter and its derivatives to examine the explanatory power of single-frequency and multifrequency models with respect to the mean sediment grain size obtained from the grab samples. A strong and statistically significant (p < 0.05) correlation between the mean backscatter and the absolute values of the mean sediment grain size for the data was noted. The root mean squared error (RMSE) values identified the 30 kHz model as the best performing model responsible for explaining the most variation (84.3%) of the mean grain size at a statistically significant output (p < 0.05) with an adjusted r2 = 0.82. Overall, the single low-frequency sources showed a marginal gain on the multifrequency model, with the 30 kHz model driving the significance of this multifrequency model, and the inclusion of the higher frequencies diminished the level of agreement. We recommend further detailed and sufficient ground-truth data to better predict sediment properties and to discriminate benthic habitats to enhance the reliability of multifrequency backscatter data for the monitoring and management of marine protected areas.