A latest update indicated that some 45,000 people in Niger have been forced to leave their homes, almost twice that of an estimate of 24,000 released earlier Tuesday.
Heavy rains forecast to last until September are also expected to excerbate the food crisis which had already hit the region as crops were washed away.
"West Africa's annual floods bring with them not only the threat of vector-borne and communicable diseases, but it further endangers the lives of people already malnourished by the food price crisis," said Eric Laroche, Assistant Director-General of the WHO's Health Action in Crises Cluster.
Cholera is already appearing in the region.
In Benin, there have been 192 cases of cholera since July 24, one fatal, WHO spokesman Paul Garwood told AFP.
In Guinea Bissau, 2,018 cases of cholera were recorded, with 41 deaths.
The WHO said Benin, Togo, Niger, Mali, Mauritania and Burkina Faso were in need of urgent aid.
In these countries even infrastructure needed for aid delivery, such as bridges, roads and railway lines, have been destroyed by the floods.
In Togo, nine bridges and more than 1,500 homes have been destroyed, said Garwood.
"Many roads in the region are inaccessible due to the floods," he added.
The situation was worsening the food crisis already being felt in the region.
"The biggest problem is the combination of floods and the food crisis," said Garwood.
Families had yet to recover from the floods last year during which swathes of farm land were destroyed and leading to a shortage of food, he explained.
"This year's floods just compound the problem," said Garwood.
While about 76 million dollars was needed for emergency health care for the region, only 22 percent of this sum has been met so far, WHO added.