The British charity warned that the rains are "showing no signs of slowing down."
Several nations in the Horn of Africa region, particularly Kenya, Somalia and Ethiopia have been lashed by unrelenting downpours since the beginning of the month due to the El Nino weather phenomenon. The rains have inundated homes and farmland.
Save the Children said 46 people had died in Kenya, 32 in Somalia and 33 more died in Ethiopia,.
Xavier Joubert, Ethiopia's director for Save the Children said heavy flooding and displacement have cut off families and children from basic services, including access to food, health care, water and hygiene services.
"With that comes the real risk of waterborne diseases including cholera and measles," Joubert said.
Humanitarian groups have warned that the situation is only likely to worsen and called for urgent global intervention as El Nino is expected to last until at least April 2024.
El Nino is typically associated with increased heat worldwide, as well as drought in some parts of the world and heavy rains elsewhere.
The Horn of Africa is one of the most vulnerable regions to climate change and extreme weather events are occurring with increased frequency and intensity.
At the end of 2019, 265 people died and tens of thousands were displaced during two months of relentless rainfall in several countries in East Africa.
Between October 1997 and January 1998, devastating floods caused by El Nino led to more than 6,000 deaths in five Horn of Africa nations. At least 1,800 people died in Somalia where the Juba River burst its banks.
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