Yorkshire Water said the problem was detected at water treatment works at Tophill Low and Keldgate.
A spokesman said the issue had now been resolved but it could take several hours for water supplies to return to normal.
The HU7 and HU8 postcodes were particularly affected by the problem, along with other places in the city.
Tens of thousands of residents could be affected, but the exact figure will not be known until an investigation has been carried out.
Yorkshire Water said: "We apologise for the inconvenience caused this morning and hope to get the issue resolved and the water supply back to normal by the end of the day."
Thousands of homes in Hull have been left without water due to a technical fault.