Local officials told media that 43 people died in Jowzjan province, 33 in Faryab province and six in Sar-e Pul province.
The floodwaters swept through villages and fields, engulfing thousands of homes and leaving many people seeking safety on the roofs of their mud-brick houses.
“We have been able to recover 43 bodies,” Jowzjan provincial police chief Faqir Mohammad Jowzjani told media.
“Rescue helicopters have evacuated some 200 people, but many people are still trapped on roofs of their homes and some are also missing.”
Faryab governor Mohammadullah Batash said the death toll in the province, which borders Turkmenistan, was expected to rise.
“We have a confirmed toll of 33 people dead and 2,152 houses destroyed, several districts have been badly affected,” he said. “Rain is still continuing, which is hampering relief efforts.”
In Sar-e Pul, another northern province, the flooding killed at least six people with more than a dozen still missing, said governor Abdul Jabar Haqbeen.
The floodwaters destroyed farmland and also killed livestock across the remote region.
Flooding often occurs during the spring rainy season in northern Afghanistan, with flimsy mud houses offering little protection against rising water levels.