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Irrigation return flow (RF) is a critical component of the water cycle in an agricultural watershed, influencing the flow regime of downstream river. As such, it should be accurately quantified when developing water resources management plans and practices. Although many studies have proposed ways to quantify RF, uncertainty in RF estimates has not been determined to improve reliability and credibility. This study examines how conceptual (CON) and physically-based (PHY) parameterization approaches affect RF uncertainty. Results showed that PHY had a smaller amount of RF uncertainty compared to CON, as parameters of the PHY approach could be regulated based on their physical meanings. This study also found that the application of constraints created based on the relationship between the conceptual parameter and physical characteristics of irrigated plots could effectively reduce RF uncertainty made using the CON approach. This study demonstrates the benefits of the physically-based parameterization approach and the application of constraints on conceptual parameters to RF estimation.