Tropical, monsoonal estuaries and rivers are highly productive yet environmentally variable systems, presenting physiological and ecological challenges for their occupants. Only a few elasmobranchs (sharks and rays) have the capacity to occupy low salinity environments for prolonged periods. Hammerhead sharks are thought to occur mainly in marine habitats, yet the ecological importance of rivers and estuaries for this group remains poorly understood. We used acoustic telemetry and river discharge data to examine residency, habitat use, and seasonal movements in three threatened hammerhead shark species in northern Australian estuaries and rivers. Great hammerheads (Sphyrna mokarran) and, to a lesser extent, wingheads (Eusphyra blochii) utilised estuarine and riverine habitats extensively, with core-use areas extending up to 22 km upstream. In contrast, scalloped hammerheads (S. lewini) were primarily confined to estuaries and adjacent marine areas. At the onset of wet seasons and a corresponding drop in salinity, wingheads and scalloped hammerheads both vacated riverine and upper estuarine habitats, while great hammerheads still occasionally occurred in estuaries and river mouths. Our findings suggest that great hammerheads are more tolerant of non-marine salinities (<30 ppt) than previously recognised, highlighting potential energetic trade-offs between osmoregulation and resource exploitation. Observations of feeding, confirmed late-stage pregnancies as well as presence of neonate individuals within the Wenlock River and Port Musgrave estuary demonstrate that these habitats are formerly overlooked yet essential habitats for great hammerheads and wingheads. With climate change increasing water temperatures and altering freshwater flows, and agricultural and industrial pressures threatening estuarine and riverine ecosystems, our findings emphasise an urgent need to preserve the integrity of these habitats to promote the recovery of these globally threatened elasmobranchs.