"Hundreds of thousands of children now displaced from their homes are facing disease, hunger from crop destruction, and disruption to their education, as schools have become crowded with fleeing families or damaged in the floods," the NGO said.
Save the Children said around 950,000 people had been displaced -- 649,184 in Niger, 225,000 in Nigeria and 73,778 in Mali.
Niger's government says more than 700,000 people have been left homeless and 273 people died since the rainy season started in June.
Neighbouring Nigeria has meanwhile seen 29 of its 36 states -- mostly in the north -- hit by rising waters of the River Niger and its major Benue tributary with the country listing 200 deaths, Save the Children said.
"According to Nigerian government data, over 115,265 hectares of farmland have also been damaged, in a country with already high rates of food insecurity," the NGO said.
The agency said one in every six children across Nigeria "faced hunger in June-August this year -- a 25 percent increase on the same period last year."
In Mali, whose government declared a state national disaster, more than half of those displaced are children, the NGO revealed.
Save the Children said climate change was seeing cases of extreme weather and its consequences grow ever more serious and frequent, with Africa suffering disproportionally.
"These countries are already ravaged by conflict and insecurity, making it even harder to respond, said Vishna Shah-Little, regional advocacy, media and communications director for the agency in Western and Central Africa.
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