The Manuherekia River could rise significantly, exceeding flows reached over the weekend, the ORC said.
While flows in the Kakanui River are also likely to increase, they are expected to remain well under the weekend's peak flows.
Rivers remain high across much of the rest of Otago; most have receded significantly and are not expected to rise significantly tonight.
Ahead of the expected rainfall, ORC staff and contractors have been working today alongside local authorities to clear debris and blockages, with a focus on Middlemarch and the Maniototo.
At the Taieri River floodbank near Otokia, the breach has been stabilised and monitoring continues.
A front, preceded by a northerly flow, moves on to the lower South Island from the Tasman Sea during this afternoon, then work its way slowly north, before weakening tomorrow morning.
The front is expected to bring a period of rain to southern New Zealand, briefly heavy in the west, with persistent falls likely about eastern areas for a time, which may be significant for areas vulnerable from previous flooding.
From 5pm until 11pm today, rain was expected for Dunedin, north of the city, as well as Central Otago, North Otago and South Canterbury, south of Tekapo and Temuka from 5pm until 11pm today.
In Westland, south of Harihari, there would be a period of rain, with some heavy falls about the ranges from 3pm today until 3am tomorrow. Rainfall amounts may approach warning criteria, especially about the ranges.
Another period of rain was likely to develop tomorrow night or early Thursday morning, and heavy falls were possible on the West Coast.
