China watershed harnessing will convert from administrative region management to water ecological management, from quality standard management to ecological health management in 12th five-year plan. On the basis of aquatic ecological function regionalization, scientific ecological monitoring and assessment is the important basic work for realization of basin water quality target. The technological route selection of water ecological monitoring and the operation key issues were studied, including water ecological characterization, selection for the monitoring index, and determination of water ecological quality anchor points, evaluation standards, determination of evaluation methods for water ecology and water ecological monitoring business operation system.