According to Environment Canada, the adverse conditions have been caused by an intense low pressure system crossing the Lower Mainland, bringing sustained downpours and powerful gusts.
In Vancouver, 15 to 25 millimetres of rain was forecast for Saturday, while on the North Shore, residents can expect up to 30 millimetres as the rain continues into the early evening.
Murray Wightman, manager of city operations in Vancouver, said the number of leaves being washed from trees is causing problems.
"We've got a number of crews out. It's mainly the leafs covering the cache basins," he said.
"We haven't got any one particular area in Vancouver that is causing us any problems, it is just scattered throughout."
The city is asking people to help clear out the fallen leaves in their neighbourhood.
In Victoria, wind speeds were expected to reach 70 km/h near Juan de Fuca Strait, while similarly strong northwest winds are attacking the Strait of Georgia over western Metro Vancouver.
Earlier on Saturday, a ferry crashed while leaving Mayne Island in the southern Gulf Islands chain, after strong winds knocked it off course and into a private floating dock.
The winds are expected to usher in cooler air for Sunday into Monday with clearing conditions, but an arctic chill in the air.