Overflowing rivers are no longer a rarity in the vast arid nation on the edge of the Sahara Desert.
But the rainy season this year has been particularly devastating, killing at least 270 people and affecting hundreds of thousands.
In Agadez -- known as the gateway to the desert -- forecasters say it's "regularly" raining, even in areas where normally "rain never falls".
Former mayor Abdourahamane Tourawa called the downpours "particularly aggressive".
"The old town in Agadez is suffering a lot of damage. Ponds are overflowing, many houses collapsed. Even the Grand Mosque wasn't spared," he told AFP.
- Collapsing -
The town, nearly 1,000 kilometres (620 miles) northeast of the capital, Niamey, was an important crossroads on the trans-Saharan caravan trade.
Atop the 16th-century mosque stands an imposing mud-brick minaret 27 metres (89 feet) tall.
The Sultan's Palace from a century earlier is testament to the past glory of the Tuaregs, known as the Blue Men due to the indigo dye of their robes and turbans.
Agadez means "to visit" in the Tuareg language, Tamashek.
Once a tourist magnet and legendary staging post on the Paris-Dakar rally when the race crossed the Sahara, jihadist attacks plaguing the region have scared visitors away.
Other gems include the house where influential German explorer Heinrich Barth stayed in 1850.
The baker's house, richly decorated with shells and arabesques, provided the backdrop for the 1990 film "The Sheltering Sky" by Bernardo Bertolucci.
"Climate change causing heavy rains represents a danger for the old town... Around a hundred houses and walls have already collapsed," town curator Ali Salifou warned.
Scientists have long warned that climate change driven by manmade fossil fuel emissions is increasing the likelihood, intensity and length of extreme weather events such as torrential rains.
- 'Under attack' -
Symbolic monuments are still "in an acceptable state" but "homes and other monuments of historic and religious value are under threat", Salifou said.
Agadez governor General Ibra Boulama Issa saw flooding for himself early this month in the grounds of the mosque, which he said would require the "reinforcement" of the building.
Recent photographs received by AFP showed its pillars eaten away by the water and houses gutted or reduced to piles of rubble.
The military-led Sahelian nation is one of several Central and West African countries hit by heavy flooding during the unusually intense rainy season.
The European Union this week released 5.4 million euros ($6 million) to help six countries affected by this year's heavy rains, of which 1.35 million euros was for Niger.
Mahamat Souleymane, the muezzin at the mosque, said the old town was at risk from the lack, or poor maintenance of, "runoff water drainage systems".
"All the jewels of our heritage are under attack from the onslaught of more violent and abundant rainy seasons," another former mayor, Rhissa Feltou, told AFP.
- Loss of authenticity -
Agadez has 20,000 residents and many hoped the 2013 UNESCO World Heritage designation would bring tourists back.
But regular upkeep and conservation requires money and the town's coffers depend on tourism revenue.
"With the little money you get here and there, you can't maintain the buildings and leave your family with empty stomachs," said Alhassane Manou, who used to sell souvenirs.
Former mayor Tourawa said Agadez's UNESCO recognition had not had "the desired effect".
"The population must benefit from projects allowing them to safeguard and maintain this architectural jewel," he said.
Beyond the climate, Agadez also faces overcrowding as a key transit hub for migrants trying to reach Europe.
Architect Abdel Rachid Idrissa Massi said overpopulation caused "exponential waste production".
He was involved in rehabilitating scores of houses and the mosque with European Union funding.
But some owners demolish the old houses to build concrete ones instead, which "distorts" the town's originality, Massi said.
The United Nations' cultural agency has also noted the trend.
Residents complain, however, that they need practical solutions.
"Those who don't want us to use modern materials in the old town must commit to come and save the town," implored Akanfaya district leader Abou Said Ahmed.
"The sealing on the houses is no longer good enough."
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