The worst-hit areas were in the mountainous Kurdistan Region in northern Iraq, where a deluge of rainwater inundated streets on Tuesday, catching residents off guard.
The two victims were trapped in their vehicle and swept away by floodwaters in Dahuk province, authorities said late on Tuesday.
In response to the crisis, local authorities across Iraq announced Tuesday and Wednesday would be holidays, mainly for schools.
At least 30 houses suffered damages from the floods in the province, Civil Defence spokesman Col Bewar Abdul Aziz told state-run TV.
Dahuk is one of three provinces that make up Kurdistan Region.
The rain, the heaviest in Iraq this winter, was accompanied by thunderstorms, which began on Monday.
The force of the rushing water washed away cars and toppled trees.
Rain continued to fall on Wednesday in some parts in Iraq, mainly Kurdistan.
Emergency response teams, including municipality workers and Civil Defence services, were on hand to rescue people stuck in cars and homes.
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