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The ataxonomic phytoplankton composition and abundance (biomass classes) in lakes of differing acidity were examined by flow cytometry. The ataxonomic parameters applied here were photosynthesis pigments and cellular protein content. Up to 1000 cells per second can be assessed by this method. Consequently, enough cells to create biomass spectra can be counted within only a few minutes. Photosynthesis pigment autofluorescence was used to separate algal cells from detritus and to classify the phytoplankton organisms into different pigment groups. Chlorophyll fluorescence ratio (CFR) at different excitation wave lengths proved to be a sensitive tool. As expected, the diversity of CFR-determined pigment groups decreased with increasing acidification. Some groups were acid-insensitive and occurred even at pH below 3.0. However, picoplanktic cyanobacteria (Synechoccocus/Synechocystis-like particles [SLPs]) were absent at pHs below 4.5–4.0, with their accompanying high metal concentrations. Thus, the reappearance of cyanobacterial picoplankton may serve as a first major restoration goal in strongly acidified lakes. Protein staining using fluorescein isothiocyanate enables fast estimates of phytoplankton biomass and establishment of biomass spectra as an estimate of the integrity of plankton communities. Although the phytoplankton investigations presented are only snapshots of the situation on the sampling days, the feasibility of flow cytometrical methods for preparing phytoplankton biomass spectra has been demonstrated. The completeness of such biomass spectra, such as the presence or absence of SLP-picoplankters, as well as the variances around regression lines (linear or parabolic), may serve as goals in restoring lakes acidified to different degrees.