The worst of the rain however is expected to strike western regions where some warnings and watches are already in place.
The falling temperatures appear to be an early indication that the El Nino system, which Niwa forecasters said continued to strengthen through July, is set to affect the early spring across the region.
El Nino, with its predominant south-westerly air flows, means the next three months are likely to see temperatures either average or below average in the Bay while rainfall is set to reduce to average or below average.
As a result, soil moisture levels and river flows are equally likely to be in the average or below average range.
During the August to October period, cold snaps and frosts can be expected in some parts of the country "from time to time".
Niwa has predicted that there is now a 97 per cent chance New Zealand will come under the climatic conditions of El Nino over late winter and early spring, and that it is "extremely likely" it will persist into the summer of 2015/16.
That would mean western regions would be wetter and eastern regions drier.
Forecaster Chris Brandolino said while it was too early to say the system could be as extreme as the El Nino which produced drought conditions in some eastern regions 18 years ago, some of the early "ingredients" were in place.
He said the main driver was unusually warm water temperatures east of the international date line.
However, a strong El Nino did not automatically mean strong impacts, Mr Brandolino said.
The situation was being monitored.