Watermelons are a natural and rich source of the non-essential amino acid L-citrulline, including the rind and seeds. Therefore, this study carried out three main tasks: i) Evaluate L-citrulline content in different parts of some watermelon types; ii) Monitor the change of L-citrulline in juice from flesh and rind at -20^oC, 0^oC, and 4^oC at the consecutive intervals of 1 day, 3 days, 6 days, 10 days, 15 days and 21 days; iii) Investigate the effect of fresh cut watermelon (skin and flesh) at storage time on the L-citrulline content. UV-vis absorption spectroscopy method was used to determine the L-citrulline content at 490 nm. As a result, the content of L-citrulline in the rind ranged from 0.764 to 1.277 mg/g, which was greater than that of L-citrulline in watermelon flesh (0.580 to 1.103 mg/g), seeds (0.179 to 0.214 mg/g) (dwt) and similar among three types of watermelons. However, L-citrulline in rind juice was more affected by storage temperature and time than L-citrulline in fruit juice at the same freezing temperature. In contrast, the fresh-cut watermelon rind had less L-citrulline content reduction than the fresh-cut watermelon at -20^oC for a longer time. These results indicated that watermelon rind, an agricultural waste rich in natural citrulline, should be exploited. Finally, the low temperature below 4^oC influenced the L-citrulline content in watermelon, so watermelon juice and fresh-cut watermelon rind will be suitable for long-term freezing.