This data set contains: (1) Chla_PhytoPAM: Chlorophyll a fluorescence data measured by PhytoPAM device for all replicas and experiment conditions on the green alga Scenedesmus costatus, the diatom Gomphonema parvulum and the cyanobacteria culture Phormidium sp. and Microcystis aeruginosa, (2) Yield_PhytoPAM: Effective quantum yield data measured by PhytoPAM device for all replicas and experiment conditions on the green alga Scenedesmus costatus, the diatom Gomphonema parvulum and the cyanobacteria culture Phormidium sp. and Microcystis aeruginosa., (3) Data_cellular_density_GREEN, Cellular density for the green algae Scenedesmus costatus experiment. Chlorophyll a concentration by cell were calculated directly in RStudio., (4) Data_FAMEs, Data of relative percentage of each fatty acid for both TAGs and polar lipid fractions for all replicas and experiment conditions., (5) Data_lipids, Lipid content for all replicas and experiment conditions. (6) Prise_essai_tot, Weighed mass of culture used for lipid extraction for all replicas and experiment conditions., (7) Nutrients, Nutrients concentration for all conditions and experiments., (8) Temperature_RH, Mean and standard deviation of temperature and relative humidity data during the duration of each experiment., (9) Herbicide_concentration, Herbicide concentration for both abiotic and biotic conditions and for all replicas and experiment conditions. In addition, the Metadata_file contains all the variables present in the above-mentioned files, along with their units, descriptions and comments.