The true mechanism by which iontophoresis produces clinical benefit is not always fully understood. Theoretically, the electrical current may help charged ions penetrate the skin, but actual movement of ions is rarely demonstrated.

Indeed, the prime use today of iontophoresis may be the treatment of hyperhidrosis. A variety of drugs (generally anticholinergics have been delivered through the skin via iontophoresis to help stop sweat, and this treatment works. However, in the studies performed, the control group which received only tap water did quite well - better than merely placebo effect.

It turns out, the current itself has some therapeutic effect on hyperhidrosis, and tap water iontophoresis has gained an important role in the treatment of hyperhidrosis.

It is thought that the skin surrounding sweat glands may become hyperkeratotic, blocking the pores; this has not been properly demonstrated, and may or may not be the true mechanism.

Naturally, distilled water would not be suitable for iontophoresis, since current cannot be conducted well without ions present.