Heavy rain flooded parts of Courtenay on Vancouver Island on Monday. (CBC)

Another wet and windy storm rolled through B.C. overnight Monday and into Tuesday morning, leaving thousands of residents without power and many on Vancouver Island concerned about flooding.

High winds in the Fraser Valley and heavy snow in the Prince George area knocked out power to about 40,000 B.C. Hydro customers overnight, but crews expected to restore service in most areas by later Tuesday morning.

Wind and rainfall warnings were lifted for Metro Vancouver and Victoria early Tuesday, but remained posted for most of Vancouver Island and southern B.C.

The weather was expected to ease Tuesday, but another strong storm was forecast to blow onto the coast Wednesday.

A local state of emergency remained in effect in Courtenay on Vancouver Island after heavy rain led to some flooding Monday, but by 7 a.m. officials were saying they did not expect more flooding on Tuesday.

The rising water closed many roads, bridges, businesses and schools in Courtenay on Monday, but most of the water had receded by Tuesday morning, according to officials.

Rivers rise overnight

B.C.'s River Forecast Centre said the Nanaimo, Chemainus, Englishman and Cowichan rivers continued to rise after as much as 50 millimetres of rain fell overnight, but river levels were not expected to exceed Monday's peak.

The two storms that hit B.C. overnight Sunday and Monday brought a total of 175 millimetres of rain to the Squamish area, north of Vancouver, and 180 millimetres to the Port Alberni area on Vancouver Island.

But officials with the River Forecast Centre said the freezing level did not rise as high in the mountains as they had expected, meaning the snow in the mountains did not melt as quickly as forecast and many rivers did not rise as high as originally feared.

Highways closed

On the roads, two avalanches on Highway 99 closed the route on Tuesday morning just east of Pemberton and also between Pavilion and Cache Creek. It was not clear when the route would be reopened.

Highway 12 between Lytton and Lillooet was closed by a rockslide and there was no word on when it might reopen.

Heavy snow was reported on the Coquihalla, Highway 5, and travel on the route was not recommended.