This dataset contains raw data of craniofacial measurements from images of zebrafish larvae double-stained for cartilage and bone, whole-body calcium levels, gene expression levels, and distance moved of larval zebrafish, used for analyses and figures of the paper: Acidification, Warming, and Cadmium Exposure Disrupt Zebrafish Calcium Metabolism, Bone Formation and Swimming Activity by Geessinck et al. See the readme for a brief description of the data files and column descriptions.