Adequate aeration in deep-water culture (DWC) sustains high dissolved oxygen (DO) levels, promoting nutrient uptake and root development. In multi-layered DWC systems, where a single reservoir supplies multiple trays, strategic aeration placement is essential for uniform oxygen distribution. This study examines how aeration location (reservoir vs. growing tray) and oxygenation method (air pump vs. oxygen concentrator) affect root zone DO levels and the growth of arugula (Eruca sativa ‘Astro’) and spinach (Spinacia oleracea ‘Auroch’). Plants were grown for 25 days in an indoor vertical farm at the air temperature of 22 °C under sole-source LED lighting (18-h photoperiod, 215 µmol∙m⁻²∙s⁻¹). Six aeration treatments were applied in a DWC system comprising a reservoir and a growing tray: no aeration (control), air pump aeration (reservoir, tray, or both), and oxygen concentrator aeration (reservoir or tray). The average DO level in the rootzone without aeration was 5.6 ppm. Aeration using the air pump increased DO to 6.0 ppm when placed in the reservoir, 7.3 ppm when placed in the tray, and 7.3 ppm when applied to both the reservoir and the tray. The oxygen concentrator treatment resulted in a higher increase in DO in the root zone, reaching 9.5 ppm when aeration was applied in the reservoir and 19.7 ppm when applied in the growing tray. Regardless of the oxygenation method, aeration in the reservoir had no effect on the growth of arugula or spinach compared to no aeration. Air pump aeration in the growing tray or both locations similarly increased leaf area, shoot fresh mass, and shoot dry mass in both species. In arugula, leaf area, shoot fresh mass, and shoot dry mass increased by 294%, 227%, and 120%, respectively. In spinach, leaf area, shoot fresh mass, and shoot dry mass increased by 184%, 216%, and 100%, respectively. Oxygen concentrator aeration in the growing tray increased leaf area by 217%, shoot fresh mass by 224%, and shoot dry mass by 73% in arugula, while having minimal effects on spinach. Our findings indicate that aerating the growing tray is more effective at increasing DO concentration than aerating the reservoir. Additionally, oxygen concentrators were more efficient than air pumps at elevating DO levels. However, regardless of DO concentration, aeration in the growing tray with the air pump was most effective at promoting growth in both arugula and spinach.