The main routes out of the city of about 1.5 million are mostly under water, and about 11,500 of its inhabitants have been affected by the disaster.
Over the past three months, the rains have caused 217 deaths across the country and affected more than 350,000 people, according to the military government.
Niamey, in the southwest of the country, was initially spared, but now canoes have replaced buses and delivery vans on the roads.
To reach other parts of the country, "you have to take a canoe and hope to find a vehicle on the other shore," explained Habiboulaye Abdoulaye, a resident of a suburb totally surrounded by water.
Most transport companies have suspended their routes to the rest of Niger.
Watching a torrent of mud flow on the edge of the city, desperate driver Ali Adamou told AFP his truck had been "engulfed by the waters" along with four others.
"I was almost killed when a minibus sank," Adamou added.
Restoring roads
Along with dilapidated dinghies that charge 500 CFA francs a ride (a little less than $1), gendarme and military motorboats are helping to transport stranded residents.
To the east of the capital, French construction group Sogea-Satom is working to re-open National Route 1, the country's principal highway that runs for almost 1,500 kilometres.
On the banks of the Niger River in Niamey, excavators were at work to raise the dykes, while volunteers and soldiers rushed around to seal cracks with sandbags.
The Tera-Niamey highway, the only truck route between the capital and the north of Burkina Faso, recently reopened.
"The state is doing everything to restore traffic," Colonel Salissou Mahaman Salissou, the minister of transport said.
The authorities fear that an extended transport interruption will lead to shortages, especially of fuel.
