The water in your house should be crystal clear and without smell. When you start seeing small black particles in your bathtub, toilet and faucets, it is a sign that there is a problem with your plumbing.
Black specs in waters are often caused by the deterioration of rubber in flexible water pipes (water heater, sink faucets and toilets), washers and O-rings. They could also be caused by minerals deposits, pipe corrosions, corroded water heater or sand/silt from a well.

Black specks in water do not pose any danger especially when they are traces of minerals like manganese or iron. Rubber particles if ingested will not be digested by your stomach and will pass through your digestive system. You should however avoid drinking it and have quality tests done.
The small black specks can also clog your faucet aerators and shower heads. If you look at the tip of your kitchen/bathroom faucet, you will see a small attachment with a fine nozzles. That is called a faucet aerator. It prevents water from splashing back.
Due to the size of the holes in the faucet aerators and shower heads, these particles will clog them up. If you do not fix the problem as fast as reasonably possible you will notice that your shower and kitchen/bathroom faucet pressure will be impaired.
To get rid of black specks in water, you will need to replace the flexible water supply pipes, water filters or just let the water run out for a few days in case of a new well. Old galvanized steel water pipes will need to be replaced. A water heater older than 15 years will also need a replacement.
Troubleshooting the Black Specks in Water Problem

The first thing you need to ask yourself once you start seining the black specs in your water is whether the problem is affecting both the cold water and the hot water. Another thing you need to determine is if it is affecting only one fixture or all the fixtures in your house.
1. Black Specks in Hot Water
If the black specs are only on the hot water line, the problem is most likely your water heater. Your water heater has a lot of sediment which sit at the bottom of the tank. When agitated, the particles can rise up and flow out of the tank through your hot water supply pipe.
A corroded water heater can also be the source of the black specs in your water. Although most of the time the rust particles are brown, they could also be black.
A water heater tank has a sacrificial anode rod that reacts with elements in the water. In the process, the anode rod wears out and a replacement would then be needed.
If the anode rod is not replaced, the elements in the water will start reacting with the inner lining of the tank thereby exposing the steel to corrosion. This could be the source of the black specs in the water. More on water heater anode replacement here.
You are also advised to flush your water heater at least once per year. This helps to remove most of the sediment. Failure to flush your water heater will lead to a buildup of sediment in the tank and when agitated by incoming cold water could cause them to move up and flow out through the hot water pipe.
Another common culprit of black specks in your hot water is the hot water supply pipe from the water heater. If you have a stainless steel flexible hose pipe carrying water out of the water heater, the inner lining of the hose which is made of rubber could be disintegrating and hence the black specks.

If your water heater has these flexible hoses instead of the solid copper pipes, I would suggest that you replace them. These are really cheap and easy to replace.
Another thing you can try to do is flush out the water heater. I have written a detailed post on how to flush sediment out of a water heater. Read it here.
If your water heater is 10 or even more years old, you will need to replace it. I have written a post explaining the signs that show your water heater needs to be replaced. Read it here.
2. Black Specks in Toilet Bowl
Black specks/spots in toilet bowl could be cause by rubber parts deterioration, minerals deposits or even mold. If you rarely use the toilet or the black spots are above the waterline, it is most likely mold.
To get rid of the mold, flush the try and try to force as much water as possible out of the bowl using a plunger. Pour 2 cups of vinegar in the bowl and add a cup of baking soda or half a cup borax.
Swish the solution around the bowl with a toilet brush. Wait for a few hours while frequently swishing the solution around to keep the bowl wet. Scrub the bowl with the toilet brush and removing all the black spots.
If the black specks are at the bottom of the toilet bowl, they could be caused by minerals deposits especially manganese. To fix these problem you will need to investigate the source of the minerals deposits. It will also depend on whether you use water from a well or from the city municipal.
Another thing to remember is that your toilet has a lot of rubber parts inside the tank. The toilet float, flapper and other parts could start disintegrating and the specs will find their way into the toilet bowl.
You toilet also has a flexible water supply hose at the back. Although the exterior of the hose is made of braided stainless steel, the interior is made of rubber. The black rubber will after continued usage start breaking down and the specs will find their way into the toilet bowl.

A toilet water supply pipe is cheap and easy to install.
3. Black Specks in Specific Faucets
If the black specks are only in your kitchen or bathroom faucet (or any other faucet), it could be that the rubber in the water supply pipes is disintegrating. If you check under your kitchen or bathroom sink, you will see 2 hoses that bring hot and cold water to the faucet.
If the black specks appear with the cold water, it is the cold water pipe’s rubber that is flaking off. On the other hand if the black spots appear when you turn on the jot water but they do not appear in your shower or tub, the faucet hot water supply pipe is the problem.
Again, these hoses are cheap and easy to replace. I would advise that you replace both hoses at the same time.
If the black specks only appear on faucets with a filter, those could be particles from a granular activated carbon filter. In this case, replacing the filter will fix the problem.
4. Black Spots in Water from a Well
If you use water from a well and you start seeing black particles in the water, it could be sand or silt. Sand or silt particles will cause wearing out of appliances (dishwashers and washing machines) and clog most of them especially faucets, shower heads and toilet fill valves.
The solutions for such a problem are many and will vary from well to well. The best thing would be to contact a professional in water drilling to troubleshoot and give you the best solution for your well.
5. Old Galvanized Pipes
Old galvanized pipes (which are not used in modern plumbing) could be corroded and flaking off as water flows through them. It is not easy to determine if this is the problem on your own and I would advise that you work with a license plumber.
Replacing house piping is an expensive undertaking and you want to be sure if indeed that is where the problem is coming from. I have written a detailed article on why you should replace galvanized steel pipes. Find it here.