There is a 50 percent chance La Niña will be bringing cooler and windier days to the end of spring, NIWA says.
Lower than normal air pressure south of New Zealand will lead to unsettled and windy weather patterns throughout September, particularly in the west.
La Niña is part of a climate phenomenon called the El Niño Southern Oscillation (ENSO) system.
It has two opposite states - El Niño and La Niña - both of which significantly alter weather patterns across the globe.
NIWA said temperatures were most likely to be above average in the north and east of the North Island and east of the South Island.
Spells of unusual spring warmth were also likely as warm air masses from Australia occasionally flow eastward into New Zealand.
Winter snowfall, catchment-level river flows, and groundwater recharge were below normal in several regions, which could also present challenging conditions for water-reliant sectors heading into spring.