From CNN, reporter Mark Tutton relays the aid groups concern.
Philippe Conraud, Oxfam's regional humanitarian co-coordinator in Dakar, told CNN that those living in the city's densely populated suburbs have been worst affected by the flooding and are most at risk from diseases such as cholera and malaria.
"The most worrying thing for us is that people are leaving their houses and moving into schools and empty buildings, which brings sanitation problems," he said.
"If the flooding continues and nothing is done to improve sanitation then we may see diseases."
Conraud said Oxfam plans to distribute soap, detergents, mosquito nets and cooking pots to displaced people.
The United Nations reported this week that torrential rains have affected 600,000 people in 16 West African nations since June.
On Tuesday the town of Agadez in northern Niger was deluged by rainwater running down from the Air Mountains, destroying an estimated 3,500 homes and leaving 30,000 people homeless.
Giancarlo Pepe, field coordinator for Doctors Without Borders (DWB), is based in Agadez. He told CNN that the floodwater had subsided but there is now a considerable risk of malaria, cholera and measles as displaced people crowd into schools and other impromptu shelters.