Time series of average chlorophyll a concentrations within the upper 20 m of the water column measured in Lake Constance (Überlinger See) during 1980-2019. Measurements were done mostly weekly during the stratified period and less regulary during winter. No data are available form August 1983 until December 1985. In addition, this data package provides annual values of total phosphorus concentrations measured during winter mixis and average (March-May) spring water temperatures in the upper 20 m of the water column.