Based on flexible strategic management framework, the paper takes international cooperation protocols related to water from Transboundary Freshwater Disputes Database (TFDD) for example and analyzes the number of cooperation governance issues, the amount of management layers and regulators’ agencies in cooperation organization and the categories of income (cost) distribution (allocation) mode. The research demonstrates that there are some flexible features of international rivers water resources cooperation governance: riparian countries may select relative diversification governance strategies related to water, tend to construct a flexible cooperation organization featured with moderate hierarchies and simplified administrations, and adopt selective inducement modes with more flexibility to respect “joint and several liability”.