Predefined classification schemes and fixed geographic scales are often used to simplify and cost-effectively map the spatial complexity of nature. These simplifications can however limit the usefulness of the mapping effort for users who need information across a different range of thematic and spatial resolutions. We demonstrate how substrate and biological information from point samples and photos, combined with continuous multibeam data, can be modeled to predictively map percentage cover conforming with multiple existing classification schemes (i.e., HELCOM HUB; Natura 2000), while also providing high-resolution (5 m) maps of individual substrate and biological components across a 1344 km2 offshore bank in the Baltic Sea. Data for substrate and epibenthic organisms were obtained from high-resolution photo mosaics, sediment grab samples, legacy data and expert annotations. Environmental variables included pixel and object based metrics at multiple scales (0.5 m–2 km), which improved the accuracy of models. We found that using Boosted Regression Trees (BRTs) to predict continuous models of substrate and biological components provided additional detail for each component without losing accuracy in the classified maps, compared with a thematic model. Results demonstrate the sensitivity of habitat maps to the effects of spatial and thematic resolution and the importance of high-resolution maps to management applications