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Taking water institutions as an illustrative context, this paper attempts a quantitative analysis of the structural and functional linkages within institutional structure and indicates their performance implications and strategic importance for promoting institutional reforms. Against an overview of existing empirical works on institutions in general and water institutions in particular, the paper develops an analytical framework for specifying alternative models of institution-performance interaction within the water sector under different assumptions concerning institutional linkages and their structural properties. These models are, then, empirically estimated using the perception-based information provided by an international panel of 127 water experts from 43 countries and regions around the world. Based on the model results, the paper offers quantitative evidences for institutional linkages and their performance implications, and concludes by indicating their policy roles, especially in developing some reform design and implementation principles useful to overcome the technical and political economy constraints for institutional reforms.