September also marked the second consecutive month this year when global temperatures exceeded 1.5C above the pre-industrial levels, EU climate change service Copernicus said on Monday.
For western Europe it was the joint-warmest September recorded, while it was the third warmest for Europe as a whole.
Prolonged dry conditions resulted in record-low September river flows in parts of the Rhine, Danube, Vistula and Garonne-Dordogne.
Low river levels caused disruptions to navigation, water supply and agriculture in several countries, Copernicus said.
Meanwhile, around Antarctica, the sea ice extent reached its third-lowest annual winter maximum.
Copernicus director Carlo Buontempo said "exceptionally high temperatures" were experienced again across parts of Europe after an extreme summer.
"We are in a new run of months above 1.5 degrees Celsius, and with a strong El Niño still intensifying it is likely to last into 2027."
Crossing the 1.5-degree limit targeted in the Paris climate agreement was "only a matter of time", Buontempo said.
"How far we overshoot, and for how long, is still up to us."
In 2015, 195 parties adopted the legally binding Paris Agreement on climate change to limit global warming to below two degrees Celsius compared to pre-industrial levels, ideally to 1.5C.
12°C