Central Otago has had its wettest June since records began, with three to four times the normal rainfall.
The National Institute of Water and Atmospheric Research said Canterbury and Marlborough were also wetter than normal.
Heavy rain caused flooding in Otago and Southland two weeks ago, cutting off some routes between Dunedin and Oamaru for two days.
The Otago Regional Council's director of environment, John Threlfall, says with the amount of rain that came through, it's a relief there wasn't more damage.
Dr Threlfall says with warm weather now melting snow, the council is warning of swollen rivers and possible minor flooding.
In Marlborough, Blenheim had its lowest number of sunshine hours for June on record, with just 111.
The lowest temperature recorded in June was minus 12 degrees Celsius at Lake Tekapo on 28 June.