Saltwater crocodile (Crocodylus porosus) populations have recovered strongly across northern Australia over the 30 years since the species was protected from hunting. However, monitoring studies show large geographical variations in abundance across the Northern Territory, Queensland and Western Australia. The Northern Territory has considerably higher densities, raising questions about constraints on recovery in the other states. We examined broad-scale environmental influences on population abundance by modelling the species–environment relationships across northern Australia. The hypothesis-based models showed strong support for the linkage to (1) the ratio of total area of favourable wetland vegetation types (Melaleuca, grass and sedge) to total catchment area, (2) a measure of rainfall seasonality, namely the ratio of total precipitation in the coldest quarter to total precipitation in the warmest quarter of a year, and (3) the mean temperature in the coldest quarter of a year. On the other hand, we were unable to show any clear negative association with landscape modification, as indicated by the extent of high-impact land uses or human population density in catchments. We conclude that geographical variations in crocodile density are mostly attributable to differences in habitat quality rather than the management regimes adopted in the respective jurisdictions.