The fuzzy preference framework of Graph Model for Conflict Resolution (GMCR), handling both crisp and fuzzy preferences of decision makers (DMs), is capable of calculating and predicting different conflict resolutions (equilibria) according to DMs’ different satisficing criteria. Employing this methodology, a water contamination conflict occurs at the boundary of Jiangsu and Zhejiang provinces in China is investigated to provide strategic insights for both practitioners and researchers of the conflict. Additionally, a useful tool called fuzzy option prioritization, which can efficiently represent both crisp and fuzzy preferences of DMs, is introduced briefly and applied to elicit DMs’ preferences in the modeling process of the water pollution dispute. The analysis results demonstrate the applicability of the fuzzy preference framework of GMCR for systematically modeling and analyzing real-world water resources conflicts, and the usefulness of the fuzzy option prioritization technique for simplifying the process of obtaining DMs’ fuzzy preferences.