Effectively managing marine populations and predicting the future impact of human activities, requires an understanding of how sub-populations (or individual patches and structures) contribute to the health of the entire metapopulation. The theory between metapopulation persistence and connectivity has long been explored, yet rarely in complex real-world seascapes. Understanding this relationship, and the influential drivers, is essential in managing human-modified marine environments. Here we quantify the impact of connectivity and larval life history on metapopulation persistence across the complex seascape of southeast Australia. Our work coupled network approaches and eigenanalysis to efficiently estimate metapopulation-wide persistence, as well as the subpopulation contributions. Larval dispersal models were used to quantify species-specific connectivity for five important fisheries species. Eigenanalysis helped quantify overall persistence and determine the unique importance of individual sub-populations and structures. Across species and the seascape, the number of local outgoing connections was found to have the largest impact on persistence. Results also suggest the length of the pre-competency period may be critical in accurately estimating metapopulation persistence in complex seascapes. Finally, we highlight the influence that artificial structures (e.g., offshore oil and gas and wind farms) specifically may have on these dynamics.