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1 If the liver is unable to break down the ammonia it is excreted in the urine.  Other diseases - Other common causes of the ammonia smell in urine are diabetes, metabolic disorders, sexually transmitted diseases, medications, vitamins, and nutritional supplements.
Treatments for the Ammonia Smell in Urine. The treatment options for getting rid of the ammonia smell in urine is dependent upon the cause of the condition. An easy first treatment is to increase daily water intake to approximately 10 to 12 cups of water, in order to dilute the urine.