Plumbing system is unlikely to degrade the quality of your water. If you use iron pipe in your house and the system is old, you may see a discoloration (red or yellow-brown) for a few minutes after turning on the faucet. Caused by erosion of iron pipes, it is not harmful in general.
If the phenomenon happens quite often, that might result from the iron sediments in the water mains. When a surge of pressure occurs, usually from a main break or a fire hydrant being used, the sediment becomes stirred into the water. Again, a regular flushing will help correct this problem.