As top predators, crocodilians have an acute sense of hearing that is useful for their social life and for probing their environment in hunting situations. Although previous studies suggest that crocodilians are able to localize the position of a sound source, how they do this remains largely unknown. In this study, we measured the potential monaural sound localization cues (head-related transfer functions; HRTFs) on alive animals and skulls in two situations, both mimicking natural positions: basking on the land and cruising at the interface between air and water. Binaural cues were also estimated by measuring the interaural level differences (ILDs) and the interaural time differences (ITDs). In both conditions, HRTF measurements show large spectral variations (greater than 10 dB) for high frequencies, depending on the azimuthal angle. These localization cues are influenced by head size and by the internal coupling of the ears. ITDs give reliable information regarding sound-source position for low frequencies, while ILDs are more suitable for frequencies higher than 1.5 kHz. Our results support the hypothesis that crocodilian head morphology is adapted to acquire reliable localization cues from sound sources when outside the water, but also when only a small part of their head is above the air-water interface.