The Waitaki bridges in North Otago will be shut on Tuesday night due to high river levels.
The bridges near Kurow will be closed to all traffic except emergency vehicles from 8.30pm on Tuesday until 6am on Wednesday.
Transport Agency area manager Colin Hey says road user safety is paramount. Debris from flooding in January has yet to clear away.
Farmers in low-lying areas in Otago and Southland are being warned to keep an eye on stock and drivers are being told to be aware of possible flooding.[image:1207:half:right]
The Otago Regional Council says Tuesday's peak flow for the Clutha River is the highest since 1999.
The flow peaked at 1900 cubic metres per second at lunchtime, cutting roads and flooding low-lying areas in South Otago.
Regional council duty flood manager Matt Hickey says Clutha River levels will remain high for at least a couple of days as water continues to flow down from the upper catchment.
Heavy rain flooded the Pomahaka River on Monday, leaving some farmland in the Kelso area in west Otago underwater. The river peaked at 1am on Tuesday.
The council's environmental information director, John Threlfall, says south and west Otago received about 13mm of rain per hour over a six-hour period, soaking already saturated farmland.
Mr Threlfall says the council's flood alert pager system for the Pomahaka River did not work.
Kelso sheep farmer Ian Logan says he did not receive the council's flood alert and awoke on Monday to find some of his paddocks were under water.
The regional council has also been monitoring river levels following high rainfall in other parts of Otago, particularly in the Manuherikia and Kakanui catchments in Central and North Otago.
The Mataura River peaked almost 2.5 metres above its normal level at Gore on Tuesday morning.
The Southland Regional Council says the level is still rising slowly downstream at Wyndham, with an expected peak about 7pm.
The Canterbury Regional Council issued flood alerts on Monday for the Rangitata and Waitaki rivers.