We all want our restroom to be clean and that goes double for the toilet. Imagine your surprise to note the water it dingy and dirty. The commode is a naturally dirty place but the presence of discolored water probably doesn't mean you are a bad housekeeper especially if the dirty water is in the tank.
The water in a toilet tank draws from the same pipes that your other water sources utilize. It is as pure as the water that you drink and should be clear and free of contaminants. Occasionally, well water is overrun with minerals after heavy rains and the resulting water is pigmented and appears dirty. There should be no concern about this as it is simply part of a mechanism and the water is not truly dirty.
Old Rusty Tank
The ancient toilet that came with your "new" craftsman house may have seen better days. Old-style toilet tanks were not made of non-corrosive materials and they will discolor with age. Such metal-style toilets rust and leave red staining in the reservoir. All this means that the water in the tank is probably pretty disgusting looking. The good news is this water is not toxic and you can remove some of it. Pour some scale and lime remover or bleach in the tank and let it sit. Then flush and a lot of the mess will go with it.
Old houses have wonderful features, but the plumbing is not usually one of them. Often, the pipes are metal and have become corroded due to the minerals in hard water. The pipes directly deliver the water to the toilet tank and whatever is in the pipes is bound to end up in the reservoir. Although the piping problems will not affect the flushing of the commode, there is probably a plumbing project in your future to replace the corroded pipes.
Local Water Work
When the local water company does major pipe laying projects they often turn off the water at a main source. This means a back up of water and possibly contamination in the lines. The result is silty or chunky water that can give you quite a startle when it makes its way into the bowl. The water will also discolor in your taps which is more of a concern since it is for consumption. The water should clear after the pipes have been used a few times.