The water quality is generally good, but tiny parasitic worms called cercaria [1] live in the lake, which can cause cercarial dermatitis.

In 1999, when the city of Freiburg investigated the water quality of municipal lakes that had previously been quarried in, a strong eutrophication was found especially in the Flückigersee.

They state that the main reason for the nutrient pollution is an increased phosphorus content caused by inflowing groundwater.

In the summer of 2013, a diving school from Ringsheim and members of the Sea Shepherd initiated a similar clear up.

The turtles are abandoned domestic animals whose high life expectancy and food requirements endanger the ecosystem of the lake.