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The relationship between metapopulation stability and connectivity has long been investigated in ecology, however, most of these studies are focused on theoretical species and habitat networks, having limited ability to capture the complexity of real‐world metapopulations. Network analysis became more important in modeling connectivity, but it is still uncertain which network metrics are reliable predictors of persistence. Here we quantify the impact of connectivity and larval life history on marine metapopulation persistence across the complex seascape of southeast Australia. Our work coupled network‐based approaches and eigenanalysis to efficiently estimate metapopulation‐wide persistence and the subpopulation contributions. Larval dispersal models were used to quantify species‐specific metapopulation connectivity for five important fisheries species, each summarized as a migration matrix. Eigenanalysis helped to reveal metapopulation persistence and determine the importance of node‐level network properties. Across metapopulations, the number of local outgoing connections was found to have the largest impact on metapopulation persistence, implying these hub subpopulations may be the most influential in real‐world metapopulations. Results also suggest the length of the pre‐competency period may be the most influential parameter on metapopulation persistence. Finally, we identified two major hot spots of local connectivity in southeast Australia, each contributing strongly to multispecies persistence. Managers and ecologists would benefit by employing similar approaches in making more efficient and more ecologically informed decisions and focusing more on local connectivity patterns and larval competency characteristics to better understand and protect real‐world metapopulation persistence. Practically this could mean developing more marine protected areas at shorter distances and supporting collaborative research into the early life histories of the species of interest. [ABSTRACT FROM AUTHOR]