In recent years, water resources planning and management activities have expanded from narrowly focusing on flood defense, water quantity improvement and quality control to the better integration of ecosystem needs in management protocols. Because ecosystem needs are still subject to discussion, a reasonable surrogate is the use of the natural flow regime. The natural flow regime integrates ecological, geomorphic, and hydrologie functions in a watershed and provides a flow-based approach to protecting ecosystems (ecohydrology). This paper identifies a suite of ecohydrologic indicators, called the Taiwan Ecohydrology Indicator System (TEIS). This system of indicators considers seasonal change, typhoons, and ecological requirements of resident species in hydrologic indicator selection. The final set of 60 TEIS hydrologic indicators captures the magnitude, frequency, and duration characteristics of natural flow regimes. To facilitate use in policy analysis, a reduced set of indicators was selected. This set includes six parameters that can be used to minimize the complexity of optimization procedures and still reflect ecological considerations in decision making and planning.