Abstract: There is an urgent need to reduce carbon emissions in irrigation systems, as specified in China’s “Dual Carbon” goals. This study addresses the challenge of quantifying carbon emissions in the multi-water source systems of irrigation districts, particularly in terms of the fuzzy parameter uncertainties associated with water withdrawal, supply, use, and discharge. An uncertainty-based model for assessing carbon emissions was developed by incorporating scenario analysis and fuzzy set theory, and was then applied in the Zhaokou Yellow River Irrigation District. The water-energy-carbon nexus associated with different hydrological scenarios in 2015 and 2030 was analyzed. The results indicated that water consumption will increase by 21.96%—31.37% by 2030, compared to 2015, while energy consumption and carbon emissions will rise by 44.14%—46.14% and 22.89%—25.05%, respectively, with energy growth significantly outpacing water use. The major contributors to carbon emissions were found to be domestic and secondary/tertiary industrial water use. These findings provide a theoretical foundation and decision-making support for the promotion of low-carbon strategies in irrigation districts, as well as the reduction of emissions in agricultural systems.