Summary 1. Pigment analysis by high‐performance liquid chromatography (HPLC) combined with data analysis using the CHEMTAX program has proven to be a fast and precise method for determining the abundance of phytoplankton groups in marine environments. To determine whether CHEMTAX is applicable also to freshwater phytoplankton, 20 different species of freshwater algae were cultured and their pigment/chlorophyll a (Chl a) ratios determined for exponential growth at three different light intensities and for stationary growth at one light intensity. 2. The different treatments had a relatively insignificant impact on the absolute values of the diagnostic pigment/Chl a ratios, with the exception of cyanobacteria and cryptophytes for which the zeaxanthin/Chl a and alloxanthin/Chl a ratios varied considerably. 3. The pigment ratios were tested on samples collected in six different eutrophic Danish lakes during two summer periods using the CHEMTAX program to calculate the biomass of the phytoplankton groups as Chl a. The CHEMTAX‐derived seasonal changes in Chl a biomass corresponded well with the volume of the microscopically determined phytoplankton groups. More phytoplankton groups were detected by the pigment method than by the microscopic method. 4. Applying the pigment ratios developed in this study, the pigment method can be used to determine the abundance of the individual phytoplankton groups, which are useful as biological water quality indicators when determining the ecological status of freshwater lakes.