Seascape ecology studies indicate that the spatial arrangement of habitat types and the topographic complexity of the seascape are major environmental drivers of fish distributions and diversity across coral reef ecosystems. Impairment of one component of an ecologically functional habitat mosaic and reduction in the architectural complexity of coral reefs is likely to lower the quality of habitat for many fish including important fished species. Documented declines in coral cover and topographic complexity are reported from a decade of long-term coral reef ecosystem monitoring in SW Puerto Rico. To examine broader scale impacts we use reef flattening scenarios and spatial predictive modeling to demonstrate how declining seascape complexity will lead to contractions and fragmentation in the local spatial distribution of fish. This change may result in impaired connectivity, cascading impacts to ecological functioning and reduced resilience to environmental stressors. We propose that a shift in perspective is needed towards a more holistic and spatially-explicit seascape approach to ecosystem-based management that can help monitor structural change, predict ecological consequences, guide targeted restoration efforts and inform spatial prioritization in marine spatial planning.