Napier's Inner Harbour will undergo dredging for between 20 and 30 days, beginning on Monday, March 25.
A Napier City Council spokeswoman said the dredging may result in water in the Inner Harbour or the estuary appearing brown.
This was because of sediment being churned up during the dredging process.
"A programme of testing is ensuring that disturbed sediments are safe, but in the interests of safety we recommend that people stay out of the water until the water returns to normal," the spokeswoman says.
"The time it will take for the sediment to settle will depend on tidal flows and the size of the sediment particles. Steps will be taken to minimise the spread of sediment within the Inner Harbour and estuary."