Hydrotherapy is one of the primary forms of treatment that the earliest naturopaths used. While it has fallen out of fashion as a valid treatment to a great extent, it has healing potential in simply knowing how to apply water to injuries at the correct temperature, how to alternate temperature, for how long, with or without pressure, and temperature maintenance.

In the wild, animals have been observed to soak injured areas daily in local water sources until healed. At the beginning of the 20th century the most well known naturopaths, such as Benedict Lust and Henry Lindlahr, were using hydrotherapy extensively.

The famous John Harvey Kellogg of the Battle Creek Sanitarium in Michigan was known for using a great variety of hydrotherapy treatments to cure presumably "incurable" diseases. Although naturopaths are trained in hydrotherapy, many do not now use it because it can be time-consuming to perform.