Melatonin (MT) is a new plant hormone that protects against adverse environmental conditions. In the present study, the responses of Wolffia arrhiza exposed to cadmium (Cd) and MT were analyzed. Quantitative analysis of MT and precursors of its biosynthesis was performed using LC-MS-MS. The photosynthetic pigments and phytochelatins (PCs) contents were determined using HPLC, while protein and monosaccharides, stress markers, and antioxidant levels were determined using spectrophotometric methods. Interestingly, the endogenous level of MT and its substrates in W. arrhiza exposed to 1–100 µM Cd was significantly higher compared to the control. Additionally, the application of 25 µM MT and Cd intensified the biosynthesis of these compounds. The most stimulatory effect on the growth and content of pigments, protein, and sugars was observed in plants treated with 25 µM MT. In contrast, Cd treatment caused a decrease in plant weight and level of these compounds, while the application of 25 µM MT mitigated the inhibitory effect of Cd. Additionally, Cd enhanced the level of stress markers; simultaneously, MT reduced their content in duckweed exposed to Cd. In plants treated with Cd, PC levels were increased by Cd treatment and by 25 µM MT. These results confirmed that MT mitigated the adverse effect of Cd. Furthermore, MT presence was reported for the first time in W. arrhiza. In summary, MT is an essential phytohormone for plant growth and development, especially during heavy metal stress.