Iodine. Povidone iodine solution, to be more specific, can cause dark or black urine. This is also known as Betadine. Betadine is used topically for cleaning skin prior to surgery, cleaning wounds and for sore throat. But it can also turn your urine black. This one falls under the possibly dangerous category, because we’re just not sure how someone would get enough of it into their urine to make it turn black, unless you’re ingesting a phenomenally large amount for a sore throat… or you’re painting your body with it, which is about the only way to allow that much to seep into your skin.
Copper poisoning. Yes, the word poison sounds more Dangerous than just Possibly Dangerous, but it can be remedied if you realize what’s happening to your body. Copper toxicity takes place when your body is not able to metabolize the copper properly. This usually happens when you are ingesting large amounts of copper, or at least, more than normal. Copper can come from a few sources, but one source people may not think about is from your cookware. Cooking highly acidic foods in uncoated copper pans releases copper into your food. The excess copper can make your urine look dark green or black. Copper can also come in your drinking water. There are water test kits you can buy that will let you know if your drinking water has a safe amount of copper or too much copper.
Phenacetin Poisoning. Phenacetin poisoning can also cause black urine. It damages red blood cells (oxidation of hemoglobin), eventually, causing kidney problems. It can occur from prolonged or overdose of analgesic drugs (painkillers) that contain phenacetin. An interesting side note is that people taking phenacetin showed much higher incidents of Proteinuria than those not taking the phenacetin. Now, phenacetin poisoning is not just something that would crop up quickly. It seems to require large doses over time. If you live in the USA, and you’re not buying your meds from overseas and less than trustworthy sources, you’re unlikely to experience black urine from phenacetin poisoning today. The FDA banned phenacetin back in 1983. 
Phenol poisoning. Phenol poisoning can also cause black urine. It can come from skin contact with disinfectants. You know how some cleansers say do not allow contact with skin, wash immediately… yep, that’s what they’re talking about. Some of the more likely ways to get phenol poisoning would be by repeated skin contact, such as cleaning without rubber gloves or not washing your hands after using the cleaners… or your children crawling around on freshly cleaned floors. We’re not saying let them wallow in filth, but take caution to keep them off of freshly cleaned floors. Phenol toxicity can affect your liver and kidneys. Phenol poisoning can lead to green or black urine due to carboluria (phenol (carbolic acid) in the urine). Carboluria is due to oxidation of phenol in to hydroquinone and pyrocatechol.  Sound technical? Yeah, you’re right. It is kind of technical. To simplify, Oxidation is when a substance, in this case, phenol, is exposed to oxygen molecules, such as in air or water, there’s a chemical reaction. It’s usually slower than a magical puff of smoke, but in the essence of simplification… POOF! There you go.
Senna and Cascara. Senna and Cascara are used in laxatives. That’s right, they are poop-makers…. or rather, a poop-inducers. Both Senna and Cascara are known to help in relief of constipation. So, what do they have to do with urine? Both can cause dark urine that might be perceived as black urine. In lighter cases, it may appear light yellow brown urine. Long term use of Senna may cause liver damage.
Chloroquine - It has been used to treat malaria. It is also used as an immunosuppressant for lupus or arthritis. Chloroquine causing black urine is not in and of itself dangerous. The medicine, however, is potentially dangerous, because long term usage can result in blindness and an overdose can be fatal.
Primaquine - Here’s another medicine that has also been used used to treat malaria when other options are not available. It has also been used to treat pneumonia. And not-so-coincidentally, primaquine can also cause black urine.
Furazolidone - This is an antibiotic used to treat diarrhea, but for most people in the United States this is not likely to cause your black urine, since it is no longer available in US. Outside of the US, however, it may still be in use.
Metronidazole - Metronidazole is an antibiotic used to fight bacterial infections in GI, in the reproductive system, and in the skin. And metronidazole may also cause dark or reddish brown urine. The dark urine can easily be perceived as black urine. 
Nitrofurantoin - This medicine is used to treat a urinary tract infection. You may see it sold under brand names such as Furadantin, Macrobid, Macrodantin, Nitro Macro to name a few. Black urine, dark yellow urine or brown urine may come as a result of using one of these meds. 
Methocarbamol - This is a muscle relaxer to be used in conjunction with rest and/or physical therapy to be effective. Sold under Rabdolax or Robaxin or the combo drug Robaxisal (which contains methocarbamol and aspirin). You may not feel all that relaxed, however, when you see your black, green, or brown urine caused by the Methocarbamol. 
Methyldopa - This antihypertensive medication, sold under the name Aldomet, releases metabolites into your urine. When your urine comes in contact with bleach, presto, black urine. This is related to the L-dopa levels in your body. We’ll get into that more in the health related causes of black urine.
Excessive L-Dopa - A naturally occurring chemical in humans, l-dopa is responsible for creating dopamine and adrenaline. L-dopa is not normally created excessively by your body, but can be introduced externally and administered as medication. It is typically used to treat Parkinsons disease and the related dystonia, as long as it is dopamine-responsive dystonia.
Excessive Melanin - Hang out in the sun too much? Excessive Melanin can be caused by sun damage or overexposure to the sun. When this happens, a condition called hyperpigmentation can occur. Normally, melanin is not a problem. Melanin - this is what colors your skin and hair and what gives you freckles … and sun spots. Melanin helps protect your skin from the sun. That’s why people with low melanin, such as people with albinism need to avoid the sun. But even with that protection, the sun can still damage our skin and create Melanoma, skin cancer. Cancer causes your body to produce too much melanin, which helps explain why new dark spots may appear on your skin. Normally, there is no melanin in your urine, so if you have melanin in you pee, then your body is producing too much of it. This creates a situation called Melanuria.Too much melanin can produce dark or black urine, typically when the urine sits for a while. If you have high exposure to the sun in your job, or if you cook yourself regularly at the pool, beach, or tanning bed, and you notice black urine, you may want to test for cancer. There’s a urine test done to look for melanin in the urine, but it’s not a common test anymore as there are more advanced ways to test for cancer.
Melanogen - Think of melanogen as pre-melanin. Cancerous melanoma outputs Melanogen as well a Melanin. Melanogen, unlike melanin, is colorless, but when it enters your urine it will convert into melanin when the urine sits in the open air for a while. Melanogen in your urine is also known as Melanuria. Melanogen would be picked up as melanin in a urine test.
Alkaptonuria (also alcaptonuria) - Here’s another situation where you urine turns black after it sits in the open air for a while. This is due to homogentisic acid created by the disorder. This is caused by an inherited recessive gene disorder, a genetic defect, where your body doesn’t do a good job breaking down the amino acid called Tyrosine. Your body is lacking enough of a particular enzyme which would help the tyrosine break down properly. This breakdown occurs in your liver and it creates a by product called homogentisic acid. This particular acid is dangerous to your body. When your liver processes this homogentisic acid, it has to go somewhere. It can build up in your body tissues and joints, and it also comes out in your urine. At first your urine may appear normal, but as the urine sits in the open air, the acid creates a dark red urine, brown urine or black urine color. Since we normally don’t sit around watching our urine ferment in the toilet, we may not notice this. You might see it in a baby’s wet diaper that you didn’t get around to throwing out. As an adult you might only notice it when you start noticing other symptoms.
Some of these symptoms may include:
Can Alkaptonuria be prevented? No. It is inherited when both your parents pass the full defective gene on to you. Don’t be mad at your parents, they could not have prevented it either, unless they had recognized it earlier and decided not have kids. Then where would you be?
Can Alkaptonuria be treated? High doses of vitamin C have been shown to help slow the development of the arthritis that can come from alkaptonuria. It also seems to help reduce the skin color change that comes from the build up of the homogentisic acid , but much of this evidence is more anecdotal than deep research. In other words, you heard it from a friend, who heard it from a friend. Other than that, there’s unfortunately nothing that can be done to prevent it. Many people turn to painkillers to deal with the arthritis, and eventually joint replacement may be necessary. Anything that can be done to reduce the production and build up of the homogentisic acid would be most ideal. There are some hints of usefulness from a drug called nitisinone that is supposed to suppress the production of the homogentisic acid, but it’s only been tested in limited trial, and the results were deemed inconclusive.