The coliform threshold level is 200 bacteria per 100 ml of water, but the counts are 210 and 320 at Second Beach and Sunset Beach respectively.
"You're at a greater risk for getting a gastrointestinal illness if you do swim in the water with that level of E. coli," said Anna Marie D'Angelo, spokesperson for Vancouver Coastal Health Authority.
People are asked to obey the advisory signs and not to swim until the count drops to a safe level.
"The elevated counts are likely due to the prolonged warm weather, increased human and animal (dogs, geese, etc.) activities, particularly with the large numbers of people and boats over the last two weeks," the City of Vancouver said in a statement.
Earlier this week, weekly tests conducted by Coastal Health showed coliform counts in East False Creek were 380, almost twice the level safe for swimming and wading in the water.
It has dropped to 220 in Friday's sampling, but is still over the safe limit.
The area is used by kayakers and paddle boarders, but is not a popular spot for swimming or wading, so VCH has not posted a public warning.
Vancouver-area waters are sampled throughout the swimming season to determine compliance with the Canadian Recreational Water Guidelines.
But a researcher at the University of Windsor proposed a better system to warn swimmers about water quality at public beaches.