New data shows the water quality in the lower and middle reaches of the Yarra River is failing to meet the state government's standards, the lead advocate for the river says.

But authorities say the Yarra's water quality problems as it winds closer to suburbs and the city is consistent with the experience of other major rivers around the world, and conditions are improving.

The Environment Protection Authority has released a new online report card on the health of the Yarra, Port Phillip Bay and the rivers and creeks that flow into both. It is the first under the Napthine government's plan to improve the environmental health of the city's most famous waterways.

Despite its sometimes mixed reputation, the 2012-13 results find Port Phillip Bay in a generally healthy condition, with 60 per cent of sites monitored recording very good water quality, while 30 per cent were good and just 10 per cent fair.

But the Yarra and many other urban creeks and rivers fare worse. The data finds sites monitored along the Yarra and its tributaries below Healesville were almost universally rated fair, poor or very poor, except for a good result in Warrandyte.

In the higher reaches, largely beyond Melbourne, water quality for the Yarra and its feeder waterways, such as at Millgrove and McMahons Creek was better.

The report card consolidates monitoring at more than 100 sites across six catchments and the bay. Generally waterway health in built-up areas is significantly worse than the forested and farming regions on Melbourne's doorstep.

"Heavy rains wash litter, pollutants and stormwater into our waterways – which flow downstream and can affect water quality as far away as the Bay," the report says.

Water quality is judged on a range of factors, such as the presence of metals and nutrients. Any site rated good or above meets Victorian water quality standards, while fair, poor and below means there is some, considerable or severe stress.

The Yarra Riverkeeper Association's Ian Penrose said the report showed the river's water quality was still below legally recognised standards – known as the State Environment Protection Policies – despite some good work to improve the situation.

"Melburnians are heavily dependent on the Yarra," he said. "It is our major water source and a vital contributor to the liveability of the city. We have a responsibility to care for it better."

Environment Minister Ryan Smith said with the up-to-date data the government could target problem areas along the Yarra.

He said water quality was one test of environmental health, and surveys showed thriving populations of native species, such Macquarie perch and platypus, in Melbourne waterways. He pointed to the success of recent environmental water programs and revegetation and litter removal works.