Here is some infomation from the Australian Power and Water Corporation which may help:
"Discoloured water is usually an aesthetic issue rather than a health issue, and in all but the most severe cases the risk of illness is low".
"The corrosion of metal pipes and fittings installed in household plumbing systems can discolour drinking water. Older homes [...] may have galvanised iron pipes in their plumbing systems which may have rusted. This can cause drinking water to be brownish in colour and contain visible particles".
"Discoloured water is most common first thing in the morning when there has been no water used overnight, or if the house has been left vacant for a while. This also occurs at seldom-used taps. The water should run clear after flushing the tap for a couple of minutes. If this problem occurs in conjunction with a noticeable reduction in water pressure, the pipes may need to be replaced."
"To check if there is corroded galvanised pipe in your plumbing system, compare water samples from a front tap near the water meter and from a rear tap at the back of your house or in the backyard. If the water from the front tap is of noticeably better quality than that from a rear tap, this indicates there is corroded galvanised iron pipe in the plumbing system."
"If the sample from the tap is initially discoloured and becomes clear after flushing, then all or part of the pipe before this point could be galvanised. If the water does not become clear then the problem is likely to be more widespread and occurring in other homes in the area. Normally this will only occur for a short time, however, if it persists, contact [your water service provider]."
"Corrosion is accelerated in hot water systems. If the cold water is clear and the hot water is brownish in colour or contains noticeable particles this suggests corrosion of the hot water system. Flushing the hot water system may help to clear out the sediment buildup in the bottom of the tank. Always be careful when working with hot water systems, and you should consider consulting a plumber."
Source: Power and Water, 2010 - http://www.powerwater.com.au/__data/assets/pdf_file/0013/2632/water_quality_problems.pdf
If this is a recent change, you may also want to look at the source of your water & whether it or its fundamental chemistry has changed.
A water utility I was once with had an issue when they changed from a high dissolved oxygen source to a low dissolved oxygen source. The old galvanised mild steel pipes were used to a certain level of oxygen in the water. When the oxygen levels dropped the rust in the pipes started to dissolve causing a fairly major incident as customers understandably didn't want to drink the water.
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