Local police said some 50 people were still missing after the flood hit on May 19 in the Sayyad and Shar-e Naw districts of the northern Sar-e Pol Province.
They added that thousands of people had taken shelter in mosques and schools.
Afghanistan's harshest winter in some 15 years saw unusually heavy snowfalls, with experts predicting that rivers overflowing by melting snow were likely to flood in the mountainous north during spring.
According to IMMAP, a data-analysis and mapping company, 15 percent of Afghanistan's population is at high risk of being affected.
In March, the UN humanitarian office for Afghanistan said at least 145 people were missing and "presumed dead" after an avalanche hit a remote village in northeastern Badakhshan province.