After heavy dumpings of rain up north over the past few weeks, it was the South Island’s turn to get a drenching.

Some farmland in West Otago was particularly hard hit, with areas near the Pomahaka and Clutha Rivers flooded after a six hour deluge on Monday.

The regional council has been monitoring river levels closely after several slips and surface flooding cut roads overnight.

Council Environment Information Director John Threlfall says farmers in particular should be on high alert, particularly in pasture areas near river banks.

"I believe some of the land there was recently ploughed so there could well be some sedimentation issues, sediment moving around.

"So they will be looking now as the waters drain away just to see what damage has been done.

"I believe there were no stock issues, either they were cleared in time or they were able to clear them out when the water was low lying."

Mr Threlfall says many farmers weren’t alerted in time to take the proper precautions after flood warning systems failed.

"It was just one of those quirky situations that we had one little part of our system which let us down; we have already put a fix in there to make sure that it doesn’t happen again."

Canterbury and Southland Councils are also issuing warnings to farmers near at risk rivers, as rain continues over Tuesday.

Keep up to date with the weather in your region and warnings on Philip Duncan's site: weatherwatch.co.nz