A fairly large crocodile species, the American crocodile has a stocky body with a long, powerful tail. The short but muscular legs end in sharp claws and the long triangular snout contains 14 to 15 sharp, conical teeth on each side. The large fourth tooth of the lower jaw fits into a pit in the upper jaw, but remains visible. The American crocodile is neatly adapted to life in the water. The ears, eyes and nostrils are located on the top of the head so that nearly the whole body can be submerged. A fold of skin can close the windpipe to enable the crocodile to open its mouth underwater and breathe through the nostrils. The eyes can be covered with a third eyelid to protect them underwater and the ears are covered with a flap of skin. The pupils are vertical slits to help with night vision and there is a distinct swelling in front of each eye.

Very young American crocodiles are green with dark banding on the back and tail. Juveniles are olive green and are no longer banded. Adults are dull grey, with a white to yellow belly. Compared with other crocodile species, the armour is less prominent. Rows of raised scales contain knobs of bone.