The internal anatomy of the manatee has been well understood for over a hundred years, but for many organs and organ systems, modern histological and histochemical techniques need to be applied to understand their function or physiology.

Manatee senses are well-developed, especially hearing which has been measured as a range exceeding that of humans in the low frequency range. Touch, taste, sight, and smell are all important senses for the manatee and appear to be well-developed. Further studies are in progress to determine ranges of sensitivity.

Digestion in manatees typifies the hindgut digesters, herbivores in which most cellulose breakdown occurs in the large intestine. The horse is another hindgut digester.

Kidney function in manatees has not been studied, but most scientists believe that manatees can exist for some time without fresh water, but that the animals must have access to freshwater periodically to survive. Preliminary studies suggest that manatee kidneys can produce a reasonably concentrated urine.