<p>The water, energy, and food (WEF) sectors are closely interconnected, and quantifying these interactions is especially critical in transboundary river systems where upstream and downstream regions often face water allocation conflicts. In addition, agricultural activities—particularly crop cultivation and livestock production—further exacerbate water quality degradation through increased nutrient loading and coliform contamination. The Peace River Basin (PRB) in Canada exemplifies these challenges. In this study, we developed a WEF nexus model based on the Bayesian network (BN) approach to analyze causal relationships between the influencing and target variables, identify the key influential factors, and evaluate trade-offs. The model shows acceptable performance, with error rates of 24.3% for crop yield, 32.9-36.8% for seasonal hydropower production, and 22.5% for water quality. Results show that water quality is highly sensitive to total phosphorus concentration. The scenario of intensified agriculture (increased nutrient inputs, expanded cropland, and greater livestock numbers) has the potential to more than double crop production, but is likely to deteriorate water quality by raising the likelihood of marginal and fair water quality from roughly 1/4 to 3/5. Specifically, livestock and cropland expansion show the most pronounced effects, increasing this likelihood by 24.3% and 17.7%, respectively. A more balanced reservoir operation—with a higher ratio of water release during the open-water season relative to the freeze-up season—increases downstream flow by 8.5% while maintaining annual hydropower generation. This study provides insights into economic improvement and environmental sustainability to inform integrated resource management.</p>