Ammonia (including NH₃ and NH₄⁺) is a major pollutant of freshwater environments. However, the toxic effects of ammonia on the early stages of fish are not fully understood, and little is known about the effects on the sensory system. In this study, we hypothesized that ammonia exposure can cause adverse effects on embryonic development and impair the lateral line system of fish. Zebrafish embryos were exposed to high-ammonia water (10, 15, 20, 25, and 30 mM NH₄Cl; pH 7.0) for 96 h (0–96 h post-fertilization). The body length, heart rate, and otic vesicle size had significantly decreased with ≥15 mM NH₄Cl, while the number and function of lateral-line hair cells had decreased with ≥10 mM NH₄Cl. The mechanoelectrical transduction (MET) channel-mediated Ca²⁺ influx was measured with a scanning ion-selective microelectrode technique to reveal the function of hair cells. We found that NH₄⁺ (≥5 mM NH₄Cl) entered hair cells and suppressed the Ca²⁺ influx of hair cells. Neomycin and La³⁺ (MET channel blockers) suppressed NH₄⁺ influx, suggesting that NH₄⁺ enters hair cells via MET channels in hair bundles. In conclusion, this study showed that ammonia exposure (≥10 mM NH₄Cl) can cause adverse effects in zebrafish embryos, and lateral-line hair cells are sensitive to ammonia exposure.