Connectivity is central to coastal freshwater fish conservation. Resident species in coastal freshwater systems depend on longitudinal river networks that maintain access to upstream and downstream habitats, while diadromous species require movement pathways linking rivers, estuaries and the sea. Despite this, spatial conservation planning often treats freshwater, estuarine and marine habitats as separate planning domains, limiting its ability to identify priority areas that maintain the connected habitats needed by coastal freshwater fishes with different connectivity requirements. This study evaluates how different connectivity assumptions influence conservation planning for coastal freshwater fish in south-eastern Australia. Using catchments associated with stream segments as planning units and habitat suitability models developed for coastal freshwater fish, spatial prioritisation was performed using the Prioritizr package in R to compare three planning scenarios. The spatial prioritisation identified planning units that represented at least 30% of each species’ distribution, while minimising conservation cost and favouring structural connectivity for target species. The first scenario focused on resident freshwater fish and used longitudinal freshwater connectivity among upstream and downstream planning units. The second scenario tested how priorities changed when planning focused on diadromous species and incorporated connectivity across freshwater, estuarine and marine systems. The third scenario tested how priorities shift when resident freshwater and diadromous species were planned together by representing each species group’s connectivity requirements. By comparing these scenarios, we show how life-history-specific connectivity requirements change the location, configuration and cost of selected planning units. Our results demonstrate whether planning for resident species alone is sufficient to capture the conservation needs of diadromous species and whether an integrated cross-realm approach can support both longitudinal freshwater connectivity and cross-realm movement pathways. This framework has the potential to support conservation efforts by identifying priority habitat networks for coastal freshwater species.