This dataset contains morphological observations of zebrafish embryos from toxicological experiments from the department of Ecotoxicology at the Helmholtz-Center for Environmental Research (UFZ). Data was recorded via INTOB, a software to collect and manage data and metadata from toxicological observations. The dataset contains two directories, data/which contains experimental data, and scripts/ which contains all code needed to run the analysis described in the paper, as well as a compiled HTML file. results/ contains a table with EC50 and LC50 values as visualised in Figure 3 of the paper. data/intob_data/ contains several csv files: effect_list_info.csv contains all possible effects of the database and their relation to each other obs_phenotypes.csv contains all individual observations metadata.csv lists metadata about the experiments and substances plate_layout.csv contains experimental setups, i.e. layouts of substances and concentrations in well-plates or vials phys_chem_prop.csv contains the physico-chemical observations of the substances data/data_for_analysis/ contains files required in the script and data/zotero_phenotype_library/ contains the results of the literature review described in the paper in JSON format.