Water stress conditions caused by climate change and low soil water retention are major threats to agricultural production. It is a widely accepted fact that soil containing more organic matter has higher water holding capacity, which in turn affects plant water use efficiency (WUE). However, related research is under water stress conditions in horticultural crops is limited. In this study, we applied 50% (deficit) and 100% (well-watered) evapotranspiration (ET) irrigation rates in the field, with or without humic substances residuals in the soil (HS or control), and tested the effects on seedless (triploid) and seeded (diploid) watermelon (Citrullus lanatus) yield, quality and soil property changes. Deficit irrigation decreased triploid and diploid watermelon total yield by 19 and 23%, respectively. HS significantly increased triploid watermelon early yield by 73% compared to control, especially under deficit irrigation (115%). HS also increased triploid total marketable yield by 20%. Compared to the well-watered treatment (100%-ET), deficit irrigation (50%-ET) decreased yield of mid-size triploid (5-9 kg) and large-size diploid (>9 kg) watermelon fruits; while HS increased yield of large-size fruit (>9 kg) in both triploid and diploid watermelon compared to control. Neither HS nor irrigation affected watermelon quality, except that 100%-ET irrigation rate significantly decreased triploid fruit firmness in the control, but not in the HS treatment. HS significantly increased soil organic carbon (24%), which was positively associated with WUE for triploid watermelon (P=0.02). These results indicate that soil organic amendments with humic substances have the potential to improve plant WUE and mitigate water stress in field conditions.