The city hit 31.3C on February 4, second only to 32.3C recorded in January 1989.
The lowest temperature of the year, -0.8C, was recorded on August 15.
Meanwhile, the wettest day in Whanganui occurred 17 days later, when 43.6mm of rain fell in a 24-hour period.
November was Whanganui's wettest month of the year overall with 162mm recorded over the 30-day period.
Elsewhere around the region, Ohakune reached its lowest recorded May temperature, with the mercury dropping to -6.7C on May 22 before winter even began.
In the wind stakes, Whanganui was blown by a gust of wind measuring 94.7km/h - the most significant gust of the year - on December 1.
According to Niwa meteorologist Ben Noll, there were multiple factors driving the climate over Whanganui and New Zealand over the course of 2020.
"Generally speaking, from January through to May it was quite dry for many parts of the North Island and we saw that in Whanganui."
Noll added that by the time the rain did roll around, 2020 was wetter than usual, due to a La Nina pattern having an effect on the country's weather system.
"As we went toward the middle and later stages of the year, the Pacific Ocean went into a La Nina. La Nina can result in New Zealand turning a bit wetter, and we definitely would've seen that across New Zealand."
Asked about Whanganui reaching its second-highest recorded temperature, Noll said it was indicative of the growing presence of climate change.
"That's a trend we've seen over the years. We've seen many more record high temperatures rather than record low temperatures. That is consistent with warming climate overall."
According to Niwa, 2016 remains New Zealand's warmest year on record, with an annual nationwide average temperature of 13.45C.