Networks of small no-take marine protected areas (MPAs) are a popular approach to protect mobile marine species at key sites along their migration routes. Understanding how individuals vary in their use of these sites is needed to ensure MPA networks are optimised to offer maximum protection benefits. Using diver-led surveys, coded acoustic tags and a continental-scale collaborative network of acoustic receivers, we investigated variation in the use of three Australian MPAs by aggregating grey nurse sharks, Carcharias taurus. The Wolf Rock MPA was used year-round by C. taurus as a gestation site, with mature females spending on average 108 d (max = 254 d) at the site interspersed with 6 h–69 d absences from the MPA. In contrast, Flat Rock and Cherubs Cave-Henderson Rock MPAs were used as a transitory aggregation site with both males and females occurring at the site between June–January, only. Migratory movements ranged up to 1,500 km along the coastline, intersected 17 MPAs and/or recognised C. taurus aggregation sites, and connected temperate waters at Montague Island (31.26° S) with that of the southern Great Barrier Reef (23.40° S). Our study demonstrates how local receiver arrays and national collaborative acoustic telemetry networks are powerful tools to reveal use and connectivity of MPA networks by marine migratory species. As the east Australian C. taurus population is critically endangered and at particular risk of anthropogenic threats, ongoing monitoring of the species’ movement behaviour and complementary management outside protected area boundaries, is warranted to safeguard its protection.