The coliform counts in East False Creek are almost twice the level safe for swimming and wading in the water, tests show, with counts also inching up for Sunset Beach in English Bay.
But Vancouver Coastal Health says the danger from the contamination should not be blown out of proportion.
The risk of infection goes up once the coliform count hits 200 bacteria per 100 ml of water.
Coliform counts for East False Creek - between Science World and the Cambie Street Bridge - are 380 per 100 ml, Coastal Health says.
The area is used by kayakers and paddle boarders, but is not a popular spot for swimming or wading, so Coastal Health says they have not posted a public warning.
In 2008, the health authority warned people to avoid the area after raw sewage began flowing into the eastern edge of the creek, sending coliform levels as high as 2,900 per 100 ml.
Sunset Beach on English Bay, right off the west end in Downtown Vancouver, is just below the unsafe level at 150, as of the latest weekly sampling on July 31.
Vancouver Coastal Health says the contamination is due to boats and fecal matter from birds and geese.
The sunny weather is also playing a role, as the city has enjoyed lots of sunshine, but little rain to flush out the fecal matter.