Metal oxide nanomaterials are widely used in practical applications and represent a class of nanomaterials with the highest global annual production. Many of those, such as TiO2 and ZnO, are generally considered non‐toxic due to the lack of toxicity of the bulk material. However, these materials typically exhibit toxicity to bacteria and fungi, and there have been emerging concerns about their ecotoxicity effects. The understanding of the toxicity mechanisms is incomplete, with different studies often reporting contradictory results. The relationship between the material properties and toxicity appears to be complex and diifficult to understand, which is partly due to incomplete characterization of the nanomaterial, and possibly due to experimental artefacts in the characterization of the nanomaterial and/or its interactions with living organisms. This review discusses the comprehensive characterization of metal oxide nanomaterials and the mechanisms of their toxicity. The study of toxicity of metal oxide nanomaterials attracts huge interest due to their increasing use in various consumer products. Incomplete characterization of the nanomaterials and experimental artefacts hinder the study of the relationship between the material properties and their toxicity. Characterization methods for metal oxide nanomaterials and the mechanisms of their toxicity are discussed in this review.