Persicaria minor, locally known as kesum and belonging to the family Polygonaceae, is a widely used aromatic herb in Malaysia. Cultivating kesum hydroponically using a deep-water culture (DWC) system presents an alternative method for growers to enhance crop yields. This system delivers a liquid fertilizer solution directly to the plant roots, eliminating the need for a growth medium or water flow. Kesum contains phytochemical compounds such as quercetin-3-glucuronide and quercitrin, which have medicinal properties. The primary objective of this study was to assess the effects of nitrogen concentration on the growth, yield, phytochemical (quercetin-3-glucuronide and quercitrin) and aromatic (aldehyde and caryophyllene) content of kesum cultivated in a hydroponic system. Plants were grown under four nitrogen concentration regimes: 200 mg/L, 100 mg/L, 50 mg/L, and 0 mg/L. The experiment was conducted under a side-netted rain shelter and arranged in a Randomized Complete Block Design (RCBD) with four replications. The plants were harvested eight weeks after planting. The result indicted those supplemented with 100 mg/L of nitrogen exhibited the best growth performance and biomass yield, along with the highest levels of aromatic compounds (aldehyde C-10: 5.80% and aldehyde C-12: 12.23%). Plants treated with 50 mg/L of nitrogen produced the highest amounts of quercetin-3-glucuronide (98.261 µg/mL) and quercitrin (61.367 µg/mL) compared to other treatments. Additionally, plants receiving 200 mg/L of nitrogen had the highest caryophyllene content (12.53%). In conclusion, the deep-water culture system in hydroponics can effectively cultivate kesum, allowing for adjustments in nitrogen concentration to achieve optimal yields, phytochemical levels, or aromatic compound production based on specific objectives.