Flooding caused by extreme weather conditions in parts of Victoria reduced the water quality across popular beaches over summer, according to the environmental watchdog.

Stormwater pollution and water contamination brought on by heavy rain resulted in Geelong's Eastern Beach and Melbourne's St Kilda Beach having the worst water quality, a new report shows.

Environment Protection Authority Victoria's beach report for the 2022/23 summer revealed Eastern Beach, usually a top performer, showed less than good water quality on 47 per cent of forecasts.

Meanwhile, St Kilda, Elwood and Frankston were slightly improved, but still rated less than good 53 per cent of the time.

The highest-ranked beaches for water quality over summer were Santa Casa, which was good 87 per cent of forecasts, and Portsea (84 per cent).

The authority's chef environmental scientist, Mark Taylor, said most beaches ranked good to fair, particularly in the state's South-East and South-West on the Mornington and Bellarine peninsulas.

"Stormwater pollution following higher-than-mean rainfall in October-November, and some heavy rain events in December 2022, resulted in more 'fair' forecasts being issued this summer compared to 2021/22," Professor Taylor said.

"Eastern Beach's poorer-than-normal performance was due to floodwater contamination, but most recently the poorer water quality was caused by seagrass decomposing in the area."

The water quality at Eastern Beach has since improved and is back to normal.

The EPA's beach report service will continue through to June for the first time.