Under natural and farmed conditions, saltwater crocodiles in northern Australia nest primarily during the wet season between late-October and April. A female lays only one clutch of eggs in a nesting season with an average number of 50 eggs. The elliptical, hard-shelled eggs are an average of 8 cm in length and 5 cm in width. The eggs are laid during a single laying event, normally at night or early in the morning, into a previously constructed mound nest constructed of soil and vegetation.

In the wild, female saltwater crocodiles will reach sexual maturity at around 12 of age (2.3 metres) and males around 16 years of age (3.35 metres). In comparison, crocodiles raised in captivity reach sexual maturity at six and ten years of age, respectively for females and males. When a female first reproduces, the number and size of the eggs is small. Additionally, fertility is generally poor and survivability of any resultant hatchlings is reduced. However, after three or four breeding seasons, the number of eggs, egg size, fertility and embryo survivability increases substantially.

Most breeding animals (both male and female) on Australian crocodile farms have been sourced from the wild. More recently, farms are beginning to keep juvenile crocodiles as replacement breeding stock. This strategy will become increasingly important in the future when implementing genetic selection programs to enhance farm productivity.

Breeder crocodiles on the farm are held in a variety of pen designs including unitised pens (one male and one female), pens with one male and multiple females, and large billabongs housing large numbers of both males and females. The breeding pens with one male generally produce more fertile eggs and, therefore, more hatchlings compared to the crocodiles kept in the billabongs. The additional advantage of pens with one male is for farm management purposes where identifying the parents of hatchlings bred on the farm allows genetic improvement programs to be implemented

Breeding crocodiles in captivity poses a number of challenges. One of the biggest challenges is collecting the eggs from the nest. Only highly skilled and experienced personnel are permitted to collect the eggs. The other major challenge is introducing crocodiles to each other. The territorial nature of male crocodiles not uncommonly results in the female being killed. To overcome this problem, the females are introduced into the pen first and allowed to settle in before the male is introduced. Pens are also designed with the number of waterholes equal to the number of crocodiles destined for that pen. This allows each animal to seek refuge in a separate waterhole.