Habitat characteristics are often equated with habitat function for animals. However, in heterogeneous landscapes, similar habitat types occur in different environmental contexts. In the marine realm, landscape studies have been confined to particular environments, rather than encompassing entire seascapes, due to incompatible sampling methods required in different situations.

We examined the interactive structuring effects of local habitat characteristics and environmental context on assemblage composition.

We used a single technique—remote underwater video census—to explore the importance of habitat type (biotic structural components, substrate, and depth) and environmental context (marine vs estuarine) in structuring juvenile fish assemblages throughout an entire coastal region. In this model system, a range of structural habitat types were present in both estuarine and marine contexts.

The 1315 video surveys collected show a clear hierarchy in the organisation of juvenile fish communities, with assemblages first distinguished by environmental context, then by habitat type. Marine and estuarine mangroves contained entirely different assemblages, and likewise for rocky reefs and submerged aquatic vegetation. Our results suggest that two functionally different ‘seascape nursery’ types exist at local scales within a single region, defined by their context.

The context of a location can be of greater significance in determining potential habitat function than what habitat-forming biota and substrates are present, and apparently similar habitat types in different contexts may be functionally distinct. These findings have important implications for local-scale management and conservation of juvenile fish habitats, particularly in regard to offsetting and restoration.