Nature-based solutions, such as shellfish reefs, can support natural coastal defence and be a potential solution for climate-resilient shorelines in the future. In the Belgian Part of the North Sea, the “Coastbusters” projects aim to develop nature-based coastal protection by favouring subtidal mussel bed establishment on the seafloor through typical longline aquaculture techniques. Mussel beds are dependent on environmental conditions, and both influence the physical and biogeochemical features in a soft-sediment environment. Therefore, a comprehensive ecological monitoring program is essential to assess the success of future mussel bed development and its influence on the surrounding ecosystem. For establishing a monitoring baseline of the two experimental areas, a combination of conventional benthic assessment methods (grab sampling and granulometry) and non-invasive techniques (sediment profile imaging and transect diving video surveys) were utilised. Although mussel reefs did not yet develop by the time of this study, clear differences in ecological and sedimentological characteristics were found between two experimental areas (sheltered and exposed), subjected to slightly different hydrodynamic conditions. The one sheltered by coastal sandbanks was dominated by fine-muddy sand, higher species richness, biomass, and higher biological activity (burrows, fauna, and biological beds) as observed by all methods in one or another way. Moreover, functional diversity indices revealed a higher partitioning of the total available resources, suggesting more complex ecological processes in the sheltered area. Conversely, the area more exposed to the open sea was dominated by more sandy sediments, and fewer organisms were found. The combination of those different monitoring tools provides an integrated, complementary view, from different perspectives, on the biological, physical and functional characteristics of the study areas.