The research station at Winchmore, near Ashburton, recorded the highest level in a century of records, while Takaka in Golden Bay also saw its wettest April on the books.
Much of this was down to an intense low pressure system that brought widespread heavy rain and high winds on April 17, causing floods, slips and wind damage.
Going into May, the heavy rain had left soils "abnormally wet" in Tasman and Marlborough, and much of Canterbury, Niwa said.
Just a few areas, including Northland, Gisborne and Southland, failed to get a normal amount of rain across the month.
But the extra rain wasn't enough to give all farmers what they needed, and at the start of the month, soil moisture levels remained drier than normal in the Northland, Wanganui, Manawatu, Otago and Southland regions.
While April was a wet one, it was also a warm one - the nationwide average temperature of 14.5C was more than 1C above average for the month.