Context . Spread of the invasive cane toad (Rhinella marina) across northern Australia is of concern. Predator species, including the freshwater crocodile (Crocodylus johnstoni), are susceptible to cane toad toxins when ingested. Upstream populations of freshwater crocodiles are smaller than downstream counterparts because of limited resources. We measured the impact of cane toad arrival on densities of these upstream populations.

Aims . Our aim was to determine whether the influx of cane toads had a negative impact on populations of upstream ‘stunted’ freshwater crocodiles.

Methods . Population surveys for crocodiles were conducted in three upstream creek systems, using day- and night-based survey methods, before the arrival of cane toads in the area. These surveys were repeated under similar conditions following the arrival of cane toads, to compare the distribution and densities of freshwater crocodiles and, hence, measure the impact of cane toads.

Key results . There were significant declines in crocodile density at two survey sites following the arrival of cane toads, and we found dead crocodiles and cane toad carcasses with crocodile bite marks. The third site showed no change in density. There was a decline in mean density across all sites from 3.0 crocodiles km^–1 to 1.1 crocodiles km^–1 following the arrival of cane toads.

Conclusions . There was an overall decrease in crocodile densities and a reduction in distribution following the arrival of cane toads into the survey area. Dead crocodiles and evidence of their having eaten cane toads strongly suggest that these declines were caused directly by the arrival of cane toads into the area. One site showed no apparent change other than an increase in wariness, which may reflect the distribution of available feeding and shelter resources among the three sites.

Implications . These results suggest that upstream freshwater crocodile populations are highly susceptible to cane toad toxins, and that impacts on their population can include local extirpation. Considering their morphological and possibly genetic distinctiveness, the loss of these unique populations is of conservation concern.