As previously mentioned, one of the principles of naturopathy is "first do no harm". As a result, naturopathy is generally a non-invasive, non-toxic, natural approach to healing. Specific forms of healing used by naturopaths, however, may have minor adverse effects. If a patient is taking a homeopathic remedy, he or she may experience a temporary increase in symptoms (a "healing crisis"), which is quite normal -- this actually signals that the remedy is working. If a patient is undergoing hydrotherapy, he or she may experience light-headedness after being immersed in a hot whirlpool. Some herbs can also be toxic if taken in excessive amounts.

Some homeopathic remedies, oriental / TCM medicines, and supplements are derived from animals and may not be suitable or appropriate if you are vegetarian or vegan. Discuss this issue with your naturopath during your initial consultation.

Some herbs and over-the-counter or prescription drugs can negatively interact. Be sure to inform your naturopathic doctor as to the drugs you are taking and do not mix items before consulting with them first.

If dealing with a serious, life-threatening condition such as acute injury or trauma, naturopathic methods should not be substituted for conventional medical treatment. Naturopaths are limited in their ability to deal with such situations and it is highly recommended that you seek the services of your local hospital and/or critical care unit.