Microbiomes help maintain host health by playing key roles in immunity, energy-production, and development. These functions depend on the composition and development of the microbiome, which may in turn depend on the environment in which the host lives. For example, exposure to environmental toxins such as heavy metals may perturb a host’s microbiome, though little research has explored this potential. Drinking water contaminated with arsenic presents a global concern, affecting upwards of 65 million people in Bangladesh and West Bengal alone. Widespread arsenic contamination in rivers and riparian habitats also presents environmental and health concerns for aquatic communities. To investigate whether arsenic perturbs host microbiomes, we exposed laboratory-raised larval zebrafish populations to sodium meta-arsenite for 20 days, using concentrations of arsenic regularly observed in contaminated water.