Nine flood warnings were current across Victoria on Thursday evening, three days after the rain that produced them, with three rivers at moderate flood level and six at minor.

The Bureau of Meteorology's national warnings summary, issued at 5.40pm AEST on Thursday, lists moderate flood warnings for the Ovens and King rivers, the Loddon and the Avoca. Minor warnings cover the Latrobe, the Kiewa, the Broken, Seven Creeks, the Goulburn and the Richardson.

Two of those have come down a class. The Bureau had the Loddon under a major flood warning on Tuesday and the Ovens under a major warning at Wangaratta on Wednesday. Both now sit at moderate, which is the Bureau's classification for flooding that inundates low-lying land, cuts some roads and may isolate properties, rather than the widespread inundation major flooding describes.

The rain fell over the weekend and into Monday. In the 24 hours to 9am Monday the Bureau recorded 165.6 millimetres at Mt Buffalo Chalet, 159.0 millimetres at Handcocks and 129.0 millimetres at Strathbogie North. Wangaratta, on the Ovens, took 67.2 millimetres. Melbourne recorded 24.4 millimetres.

A moisture-laden low pressure system and its trailing cold front moved across South Australia, Victoria and southern New South Wales before tracking toward the east coast on Monday morning. Most of the water now moving through the northeast Victorian rivers fell on the Alps and the Strathbogie Ranges over that period.

The pattern is a lag rather than fresh rainfall. Alpine catchments hold and release water over days, so river heights on the Ovens, King and Kiewa peak well after the rain stops. The Bureau's flood warning service runs rainfall and streamflow observations through hydrologic models to forecast those peaks, and reissues each warning as new gauge readings come in.

Elsewhere on Thursday the Bureau had a frost warning current for the Mid North forecast district in South Australia, and a final flood warning for the Belubula River in New South Wales, which is the notice the Bureau issues when a river has fallen below the minor threshold and no further bulletins will follow. Marine wind warnings were current for every state and the Northern Territory.

No warning has been cancelled in Victoria. River heights are being read through the night and the Bureau will reissue each warning as the readings arrive. Current warnings and road closures are published at the Bureau's Victorian warnings page and at VicEmergency.