The persistent rain, with up to 100mm predicted through to 3pm today, meant some river levels were rising quickly throughout coastal Otago.
Last night, rivers on flood alert included the Waipori, Silver Stream, Kakanui, Shag, Deep Stream, Pomahaka, Waitahuna, Nenthorn Stream at Mt Stoker Rd and Taieri at Outram.
Otago Regional Council staff were on stand-by, monitoring levels closely, notifying people in affected areas and warning farmers to move stock.
The heavy rainfall could cause slips and erosion on some saturated hillsides.
Council environmental services manager Martin King said even though rivers such as the Silver Stream and the Water of Leith had dropped, they could "very quickly shoot back up again" as the rain continued.
Late yesterday afternoon the Taieri at Outram was up to its first alert, and further upstream, at Tiroiti, the level was also increasing, he said.
Rainfall sites in the hills of eastern Otago recorded more than 100mm yesterday, with the high of 211mm at The Dasher, in North Otago, in 24 hours to 4pm, and 130mm had fallen at Sullivans Dam, near Dunedin.
Dunedin city recorded 77mm in the same 24-hour period - more than the amount that fell in the April 1996 floods.
Deep Stream at State Highway 87 was rising quickly last night and had reached 129.5 cumecs at 8.30pm.
The Silver Stream, which had just about run dry before yesterday's rain, hit its first flood alert at 11am, with 44cumecs, and continued to climb to a peak of 89 cumecs in the early afternoon, before starting to drop.
Earlier, it had been expected to peak at mid-afternoon at 145 cumecs, short of the spill-over level of 160cumecs.
The regional council was urging landowners near the Silver Stream to take measures to protect their property, including storing and securing all objects that may be affected by flooding.
The Water of Leith reached a peak of 47cumecs, short of its first flood alert of 55 cumecs, about 1.30pm, before steadily dropping.
The rain had not penetrated far inland.
Ranfurly received only 12mm and Middlemarch 21mm.
