When toilet bowl water or water filling the tank suddenly turns brown, the discoloration is typically caused by rust sediment accumulating inside the toilet tank or iron mineral scale flaking off internal flush valve components. Because toilets draw water directly from your home's supply lines, brown water in the toilet also signals that sediment is present throughout your plumbing system. Alternatively, if your water heater tank is rusting internally or municipal main lines are being flushed, that discolored water enters the toilet during refill cycles. Verification: Flush the toilet multiple times to see if fresh water clears the bowl, and check other household faucets.
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