The potential toxicity of nanoparticles (NPs) to the early stages of fish is still unclear. In this study, we investigated the toxic effects of silver (AgNPs) and copper nanoparticles (CuNPs) on lateral-line hair cells of zebrafish embryos. Zebrafish embryos were incubated in different concentrations of AgNPs and CuNPs at 0˜96 h post-fertilization (hpf). Both AgNPs and CuNPs were found to cause toxic effects in zebrafish embryos in a dose-dependent manner. Values of the 96-h 50% lethal concentration (LC50) of AgNPs and CuNPs were 6.1 ppm (56.5 μM) and 2.61 ppm (41.1 μM), respectively. The number of FM1-43-labeled hair cells and the microstructure of hair bundles were significantly impaired by AgNPs [≥1 ppm (9.3 μM)] and CuNPs [≥0.01 ppm (0.16 μM)]. Ca2+ influxes at hair bundles of hair cells were measured with a scanning ion-selective microelectrode technique to evaluate the function of hair cells. AgNPs [≥0.1 ppm (0.9 μM)] and CuNPs [≥0.01 ppm (0.16 μM)] were both found to significantly reduce Ca2+ influxes. Similar toxic effects were also found in hatched embryos subjected to 4 h of exposure (96˜100 hpf) to AgNPs and CuNPs. This study revealed that lateral-line hair cells of zebrafish are susceptible to AgNPs and CuNPs, and these contaminants in aquatic environments could pose a threat to fish survival.