Migratory shorebirds such as the far eastern curlew and whimbrel undertake migrations for many thousands of kilometres across the East Asian-Australasian Flyway to breed in the northern hemisphere every year. We caught 22 far eastern curlew and 9 whimbrels from non-breeding regions from around Australia and fitted them with GPS trackers to learn about their specific migratory pathways. We compared variations in timing, routes, use of stopover sites and breeding grounds. We examined impacts of human-driven land modification in breeding and nonbreeding sites used by populations spending the non-breeding season in different parts of Australia. We determined what drives selection of flight altitude during migration. We also identified serious threats to the future conservation of these two migratory shorebirds. We found that the migration paths of these birds overlap considerably, but that birds from south-eastern Australia set off on migrations earlier and stop in more southern breeding grounds in northern China, where human modification were more substantial to their preferred habitats. Migrating shorebirds showed a preference for low altitude flight, where they expend less energy and can navigate more easily. We found a need to mitigate threats in breeding grounds, but also to protect non-breeding habitats in Australia, where these birds spend over half of each year.