A process-based understanding of community assembly at multiple scales can allow forecasting of community response to degradation and restoration practices. We draw attention to a distinct metacommunity arrangement characterised by multiple levels of assembly filters, and exemplified by freshwater habitat patches on islands. This type of metacommunity has complex spatial dynamics, and dispersal must occur across multiple intermediate habitat types. An interdisciplinary approach harnessing mathematical models and genetic tools such as eDNA and population genomics will allow us to unravel the fundamental processes acting over a large spatial and temporal scale influenced by the region's geography, historical events and species pool.