Soil organic matter degradation and water limitation caused by intense farming activities are some of the major threats affecting agricultural production. Accordingly, the concepts of sustainable agricultural systems with optimized irrigation and improved soil quality can be adapted to address these issues. During this 2-year field study, two management factors—humic substances (HS) as organic inputs (HS vs. control) and deficit irrigation as the irrigation method (50% vs. 100% based on evapotranspiration)—were evaluated based on triploid watermelon (Citrullus lanatus cv. Fascination) yield and soil property changes. HS application increased watermelon early yield by 38.6% and total yield by 11.8% compared with the control; the early yield mainly increased under deficit irrigation. Compared with full irrigation, deficit irrigation increased water use efficiency (WUE) without significantly affecting total yield. In addition, HS application significantly increased the soil organic carbon (SOC) content, which was found to be positively correlated with crop WUE. These results indicate that soil organic inputs with HS and deficit irrigation are valuable strategies to establish sustainable systems for watermelon production, which will not only increase yield and WUE but also significantly improve soil quality and save irrigation water.