Migratory species depend on connected habitats and appropriate migratory cues to complete their life cycles. Diadromous fish exemplify species with migratory life cycles by moving between connected freshwater and saltwater habitats to reproduce. However, migration increases the exposure of fish to multiple threats and it is critical that managers integrate habitat connectivity into resource management and conservation. The benefit of alternative management actions was assessed for a diadromous fish, the Australian bass Percalates novemaculeata, using a spatio-temporal population model informed by individual-based movement data. The management actions comprise seasonal closures during the spawning season, and controlling fishing pressure by limiting catch or effort. The benefits of implementing seasonal closures depend upon interactions among how fishing pressure is controlled, the response of anglers to fishery regulations and river flow regimes. The results indicated that seasonal closures are ineffective if fishing pressure is merely displaced to another location or time of year. In addition, shifting seasonal closures from spawning grounds to feeding grounds increased population abundances under low flow events when fishing effort was also controlled. However, when total annual catch is limited by a fishery closure, changing the location of seasonal closure schemes had little effect. The findings in this study highlight the need for flexible management strategies that account for migratory movements and respond both to variations in connectivity (e.g. river flow regime) and direct pressures on survivorship (e.g. exploitation). As the implementation of one management action (e.g. fishing or water regulation) could affect the influence of another management action, this study emphasizes the importance of cooperation between resource managers in conserving migratory species.