The Zambezi river, along Namibia's northeastern Caprivi Region, rose to 7.82 metres this week, its highest level in 40 years, before slightly dropping, Caprivi Governor Leonard Mwilima said.
Namibia's flood coordinator Erastus Negonga said the death toll stood at 112. Nearly 200 schools have closed, while one hospital and 19 clinics remain cut off due to floods.
In Zambia, 21 districts have been affected by flooding and the army has been called in to assist the worst affected region of Shang'ombo, where they are also helping reconstruct a bridge connecting it to the rest of the country.
In northern Botswana, rain has caused the Okavango, Zambezi and Chobe rivers to swell, leaving 430 people displaced and submerging eight villages.
The Okavango river which originates in the rain-drenched highlands of Angola empties into the desert north of Botswana, forming the Okavango Delta.
The villages of Satau and Parakarungu, with a combined population of more than 1,000, could be swept away by the rising rivers within a matter of days, a district official said.
In Mozambique, where about 4,000 people have been cut off by rising waters, emergency officials monitored Izilda, which was gaining strength in the Mozambique Channel and was likely to strike on Sunday.
Last year, heavy rains in Zambia, Zimbabwe and Malawi caused flash flooding in Mozambique that displaced tens of thousands of people and destroyed almost 100,000 hectares of crops.