Invasive predators can cause population declines in native prey species, but empirical evidence linking declines of native predators to invasive prey is relatively rare. Here, we document declines in an Australian freshwater crocodile Crocodylus johnstoni population following invasion of a toxic prey species, the cane toad Rhinella marina. Thirty-five years of standardized spotlight surveys of four segments of a large river in northern Australia revealed that the density of freshwater crocodiles decreased following toad invasion and continued to decline thereafter. Overall, intermediate-sized freshwater crocodiles (0.6-1.2m) were most severely impacted. Densities of saltwater crocodiles Crocodylus porosus increased over time and were generally less affected by toad arrival, although toad impacts were inconsistent across survey sections and size classes. Across the entire river, total freshwater crocodile densities declined by 69.5% between 1997 and 2013. Assessments of the status of this species within other large river systems in northern Australia, where baseline data are available from before the toads arrived, should be prioritized. Our findings highlight the importance of long-term monitoring programmes for quantifying the impacts of novel and unforeseen threats.