Surgical face masks are the most popularised and effective personal equipment for protecting public health during the COVID-19 pandemic. They are composed of plastic polymer fibres with a large amount of inorganic and organic compounds that can be released into aquatic environments through degradation processes. This source of microplastics and inorganic and organic substances could potentially impact aquatic organisms. In this study, the toxicogenomic effects of face masks at different stages of degradation in water were analysed in zebrafish larvae (Danio rerio) through RNA-Seq. Larvae were exposed for 10 days to three treatments: 1) face mask fragments in an initial stage of degradation (poorly degraded masks -PDM- products) with the corresponding water; 2) face mask fragments in an advanced stage of degradation (highly degraded masks -HDM- products) with the corresponding water; and 3) water derived from HDM (W-HDM). Transcriptome analyses revealed that the three treatments provoked the down-regulation of genes related to reproduction, especially the HDM products, suggesting that degradation products derived from face masks could act as endocrine disruptors. The affected genes are involved in different steps of reproduction, including gametogenesis, sperm-egg recognition and binding or fertilisation. Immune-related genes and metabolic processes were also differentially affected by the treatments.