The eutrophication of freshwater ecosystems, primarily due to human activities, leads to the proliferation of harmful algae, particularly cyanobacteria. These cyanobacteria produce highly toxic metabolites, the cyanotoxins, which have diverse effects on biological activities in aquatic organisms, including eukaryotic algae. Our research aims to understand the possible impacts of cyanotoxins on resting stage formation and maturation of algae through the example of Haematococcus lacustris, which pigment composition changes serves as an indicator of the effects of stressors on the organism. We focused on the changes on pigment and lipid contents and composition induced under cylindrospermopsin (CYN) and microcystin-LR (MC-LR) containing cyanobacterial extract exposure and their effect in Haematococcus lacustris under laboratory conditions. Post-exposure, algal biomasses were lyophilized and resuspended in dimethyl sulfoxide (DMSO) for pigment extraction, and a chloroform-methanol mixture for lipid content measurement. Pigment and fatty acid compositions were analyzed using thin layer chromatography and instrumental analytical methods, respectively. Results showed a decline in carotenoid values with increasing MC-LR concentration, indicating potential disruption in carotenoid production mechanisms. A similar trend was observed with CYN exposure. These results suggest that cyanobacterial metabolites could have adverse effects on processes related to resting stage maturation, jeopardizing the survival of the population. These findings highlight the potential ecological implications of cyanotoxin effects on algae, paving the way for further research and mitigation strategies.