The warning applies to the waterway from Prince George, and upstream.
The River Forecast Centre says water levels are expected to peak later today and overnight before slowly receding through the rest of the week.
Two waterfront parks in Prince George have been closed because of high water levels, but there is no word of serious flooding elsewhere.
A high streamflow advisory remains posted for the Lower Fraser River but flood watches have ended for the Birkenhead River through Pemberton and for the Granby River and watersheds in the Kootenay region.
High streamflow advisories have also been cancelled for several Okanagan and Similkameen-area waterways, including Mission Creek and the Kettle and West Kettle rivers as rain eases and temperatures drop after more than a week of hot weather.