We conducted a morphometric analysis of 279 Crocodylus johnstoni, using specimens from the McKinlay River (n = 265) and Arnhem Land (n = 14), to meet the management need for predicting body size of C. johnstoni from isolated body parts. The results also allow reconstruction of C. johnstoni dimensions for comparison with other crocodilian species. We detected sexual dimorphism in some body measurements from the McKinlay River, and geographic variation in the morphology of McKinlay River and Arnhem Land populations, but differences were slight. There is pronounced allometric growth in C. johnstoni in the immediate post-hatching phase, largely due to elongation of the snout after exiting the confines of the egg. We compared the size, shape and relative growth of C. johnstoni with that of other crocodilian species for which equivalent data are available, but particularly the other Australian crocodile, Crocodylus porosus. C. porosus has a proportionately longer tail and a shorter but wider snout than C. johnstoni, and we discuss possible ecological correlates of these and other differences.