Metservice predicted heavy downpours of 25 to 40mm/h in some parts of the region and further south in Auckland.
"Rainfall of this intensity can cause surface and/or flash flooding, especially in urban areas, and about low-lying areas such as streams, rivers or narrow valleys. It may also lead to slips."
The watch included a warning to motorists as driving conditions were expected to be "hazardous" with "surface flooding and poor visibility in heavy rain".
Northland police have already attended multiple minor vehicle crashes since the rain settled in on Monday.
Senior Sergeant Brian Swann, of Northland Police, said drivers needed to be cautious while driving on wet roads.
"Just a reminder for drivers about the conditions, the roads will be greasy after a long period of fine weather. Especially with this light rain, it's worse than a heavy downfall."
The thunderstorm activity should ease and move offshore into the Hauraki Gulf this evening.