If you experience diarrhea while taking magnesium supplements, it could potentially affect the absorption and effectiveness of your medication. It is recommended to take magnesium supplements with food and start with a low dose to reduce the risk of developing diarrhea. In some cases, switching to a different form of magnesium, such as bisglycinate, may also help reduce the likelihood of experiencing diarrhea. If diarrhea occurs, stopping the magnesium supplements should not cause any issues over a short period of time.