Farmers near the Kakanui River south of Oamaru have been warned to move stock to higher ground as the river is likely to flood this weekend.
MetService predicts up to 150mm of rain will fall by Sunday in northern and coastal areas of the region and in the eastern Otago hills as far as Central Otago.
Otago Regional Council says the Kakanui and Shag Rivers are of greatest concern but there is also the chance of flooding in the lower Taieri catchment.
The council's director of environmental information and science Dr John Threlfall says farmers around the Shag River have also been warned of possible flooding.
All South Canterbury rivers are in light flood conditions and are expected to continue to rise throughout Saturday.
Canterbury Regional Council says farmers near rivers need to continue to monitor river conditions and consider moving stock from low lying areas.
Emergency management officials are monitoring the situation.