The extensive alteration of freshwater habitat across the globe has resulted in the decline of a number of wildlife species, some of which now face extinction. Large-bodied species are frequently at greatest risk. However, identifying the direct and indirect pathways of impact on these long-lived and often cryptic predators has proven challenging. Since the cessation of commercial crocodile hunting in northern Australia in the 1970s, the assumption has been that populations of both the saltwater crocodile (Crocodylus porosus) and freshwater crocodile (Crocodylus johnstoni) would recover naturally. While extensive population monitoring of the saltwater crocodile has occurred, there has been limited ongoing monitoring of the freshwater crocodile to test this assumption. Moreover, there is growing concern that the increasing threat from global environmental change, including invasive alien species, anthropogenic landscape modification, agricultural pollutants, and other human activities, may jeopardise the recovery and long-term conservation of the freshwater crocodile. Here we summarise existing knowledge on the various direct and indirect threats this species faces and prioritise future actions to increase the likelihood of effective conservation outcomes for freshwater crocodiles. Although an in-depth understanding of the magnitude and dynamics of the majority of these emerging threats is still lacking, it is becoming clear that they are acting in previously unexpected ways, leading to novel combinations of cascading direct and indirect impacts.