Marine seabed mapping is an important element in marine spatial and conservation planning. Recent large scale mapping programmes have greatly increased our knowledge of the seafloor, yet at finer resolutions, large gaps remain. Loch Eriboll, Scotland, is an area of conservation interest with a diverse marine environment supporting habitats and species of conservation importance. Here we test and present strategies for a predictive seabed substrata map for Loch Eriboll using drop down Stereo Baited Remote Underwater Video (SBRUV) imagery collected as part of systematic underwater survey of the Loch. A total of 216 SBRUV deployments were made across the study site in depths of 3 m–117 m, with six seabed classes identified using an adaptation of the EUNIS (European Nature Information System) hierarchical habitat classification scheme. Four statistical learning approaches were tested, we found, Generalised Additive Models (GAMs) provided the optimal balance between over- and underfitted predictions. We demonstrate the creation of a predictive substratum habitat map covering 63 km2 of seabed which predicts the probability of presence and relative proportion of substratum types. Our method enables naturally occurring edges between habitat patches to be described well, increasing the accuracy of mapping habitat boundaries when compared to categorical approaches. The predictions allow for both defined boundaries such as those between sand and rock and fuzzy boundaries seen among fine mixed sediments to exist in the same model structure. We demonstrate that SBRUV imagery can be used to generate cost effective, fine scale predictive substrata maps that can inform marine planning. The modelling procedure presented has the potential for a wide adoption by marine stakeholders and could be used to establish baselines for long term monitoring of benthic habitats and further research such as animal distribution and movement work which require detailed benthic maps.