The ecosystem of the lake is threatened by the presence of an industrial complex and an airport close to the northern shore.

The decrease in water levels (because of construction of upstream dams and unknown causes), the increase of sedimentation (from catchment erosion), organic pollution (from food processing and Burdur City raw sewage waste), and inorganic effluent (from a sulphur mine) represent long-term threats to the integrity of the lake.

The water level has decreased from 1975 to 2002 due to the construction of dams and ponds in the catchment basin, resulting in the loss of 27% of the lake area during the period of 27 years.

Lake Burdur has great ornithological importance, harbouring numerous wintering bird species.

The formation of the lake began 5 million years ago as a tectonic depression (The burdur area is in a first grade earthquake zone).