Echuca Aerodrome recorded 44.4 millimetres in the 24 hours leading up to 9am on Thursday.
That mark surpasses our previous wettest day of the year, January 18, when 39.8mm fell in the space of 24 hours.
The rain fell as part of a cold front which swept across Victoria.
High rainfall was recorded throughout the Goulburn Valley.
Kyabram received 53mm, Lake Eppalock 73mm, Shepparton 55mm and Rochester 48mm.
In the north-west, Mildura copped 39mm and Swan Hill, just days out from its three-day annual thoroughbred racing carnival, received 35mm.
The north-east was hardest hit, with Charnwood 136mm, Archerton 134mm and Mt Buffalo 131mm, ranking highest in terms of rainfall throughout Victoria.
The downpour came just one day after the Bureau of Meteorology has moved from El Niño watch to El Niño alert, meaning that there is around a 70 per cent chance of an El Niño developing this year.
Bureau of Meteorology senior climatologist Catherine Ganter said climate models and indicators now met the bureau’s El Niño alert criteria.
“While the models show it’s very likely the tropical Pacific Ocean temperatures will reach El Niño levels during winter, we have seen some movement in the atmosphere towards El Niño conditions,” Ms Ganter said.
“While our El Niño alert criteria have been met, these changes will need to strengthen and sustain themselves over a longer period for us to consider an El Niño event.”
El Niño describes changes in the tropical Pacific Ocean that affect global weather and it occurs on average every three to five years.
During El Niño, there is a higher chance of drier weather in eastern Australia and it’s more likely to be warmer than usual for the southern two-thirds of Australia.
“The bureau’s long-range winter forecast is for drier and warmer conditions across almost all of Australia and the climate conditions in the Pacific Ocean are already factored into our forecasts,” Ms Ganter said.