While eggs are mostly laid in forest nests, they also occur on floating grass mats. Flooding often occurs on these mats, but significantly reduces the risk of predation. While forest nests also flood at times, the main risk for this type is predation.

Sex determination in the yacare caiman is based on temperature. Higher temperatures generally produce males, while lower temperatures generally produce females. A study by Zilca Campos showed that in Pantanal, Brazil, all temperatures above 31.5 degrees Celsius produced males, and under 30.5 always yielded females.