"Claims that dams in Turkey cause sand and dust storms in our geography are far from scientific," ministry spokesman Tanju Bilgic said in a statement.
Tehran on Tuesday said Turkey's upstream dam-building on shared waterways was "unacceptable", calling on its neighbour to cease such activity.
Iran has faced frequent droughts in recent years, caused in part by climate change, as well as dam-building in neighbouring countries.
"In order to prevent sand and dust storms and to mitigate their negative effects, each country must first do its part and take the necessary steps towards sustainable use of water and soil resources," Bilgic said.
"It is not a realistic approach... for the Tehran administration to blame Turkey for such problems."
The spokesman also said Ankara believed the waters shared by Iran and Turkey were "an element of cooperation rather than conflict" between the neighbouring countries.
"Turkey is open to any rational and scientific cooperation with Iran regarding this issue," he said.
Neither country is party to the 1997 United Nations Watercourses Convention that regulates the use of transnational water resources.
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