Urine with an extremely bad odor. If you observe that you are passing clouded or discolored urine, you should also check whether it has a bad odor. Urine with a very bad odor is a clear indicator of a bladder infection, as it contains dead cells or pus cells that are a result of the infection. These cells might either be your body’s own immune cells or else bacteria from the infection. In any case, it is these dead cells that cause the discoloration or cloudiness in the urine, and which is the source of the foul odor. The intensity of the discoloration and the smell is affected by the amount of water you drink, and you will find that it is far stronger when you have not passed urine for some time.