The herbicide atrazine (ATZ) is used worldwide in the control of annual grasses and broad-leaved weeds. The present study evaluated sperm quality parameters in zebrafish Danio rerio after 11-day exposure to nominal ATZ concentrations of 2, 10, and 100 μg L−1. All ATZ concentrations caused a decrease in motility, mitochondrial functionality, and membrane integrity, as measured using conventional microscopy or fluorescence microscopy with specific probes. The DNA integrity of sperm was not affected. The levels of expression of genes related to spermatogenesis, antioxidant defenses, and DNA repair were also investigated using RT-qPCR. The ATZ caused transcriptional repression of the spermatogenesis-related genes SRD5A2 and CFTR, the antioxidant defense genes SOD2 and GPX4B, and the DNA repair gene XPC. This is the first study to show that environmentally relevant concentrations of ATZ significantly affect the sperm quality in fish, possibly resulting in reduced fertility rates. In addition, we showed that the repression of genes related to spermatogenesis and cellular defense could be part of the mechanisms involved in the ATZ toxicity in the testes of male fish.