Southern, Western and Eastern train Line services face delays and cancellations.
Due to infrastructure issues, Western and Eastern Lines will experience delays of up to 12 minutes.
Southern Line services could face delays of up to 20 minutes.
The Remutaka Hill Road between Wellington and Wairarapa has reopened.
The State Highway 2 road was closed at about midday, after a truck was tipped over by strong winds near the summit.
Waka Kotahi says the truck has been recovered and the winds have eased.
A strong wind watch remains in place.
-RNZ
MetService has updated the watches and warnings on its site.
There is now a severe thunderstorm watch in place for Waikato, Waitomo, Taumarunui, Taupo, Hawkes Bay, Taranaki, Taihape, Wanganui, Manawatu, Tararua, Kapiti-Horowhenua and Wairarapa, up until 6pm Monday.
"Between 2 pm and 6 pm today, localised downpours of 25 to 40 mm/h may affect western areas of the North Island from Waikato to Horowhenua, also Central Hawke's Bay, the Tararua District, and Wairarapa north of Masterton. These downpours could occur with or without thunderstorms.
MetService said flash flooding was possible around low-lying areas.
"Driving conditions will also be hazardous with surface flooding and poor visibility in heavy rain."
It said the next update would be at 6pm.
-RNZ