A "snapshot" survey of England's largest lake found water quality is "not high" in all areas but that there was "no evidence" of problems across the whole of Windermere.
Lancaster University, which published the results, said it marked the start of a long-term monitoring programme.
Project leaders explained a fuller picture of the lake's water quality would emerge as more data is collected.
Zoologist Matt Staniek has warned sewage from waste treatment sites, septic tanks at homes and holiday lets, and run-off from farming land have contributed to a drastic deterioration of water quality.
The "citizen survey" saw about 100 volunteers gather samples from 93 sites across Windermere, Grasmere, Rydal Water, Blelham Tarn and Esthwaite Water, as well as a number of rivers and streams flowing into Windermere.
Senior lecturer Dr Ben Surridge said: "The survey emphasises that it is a mistake to think about Windermere as a single body of water with the same water quality at all locations.
"The results show that water quality is not high in all areas of the lake, but equally there is no evidence in the survey of poor water quality across the whole of Windermere.
"Understanding where there are areas of poorer water quality in Windermere is absolutely essential, if we are to identify what is causing declines in water quality and address these issues successfully."
Dr Louise Lavictoire, of the Freshwater Biological Association which is helping oversee the project, cautioned against reading too much into one set of results but said further surveys would "create a scientifically robust picture".
Blue-green blooms such as those highlighted by Mr Staniek can make humans ill and be fatal to animals. They occur naturally but are exacerbated by nutrients from phosphate in pollutants such as sewage.
The Love Windermere partnership, which includes the Environment Agency, United Utilities, the Lake District National Park Authority and the National Trust, has said it was "committed to developing the most effective solutions to maintain and improve water quality in the lake".