Nutrient criteria in estuarine waters are essential to water environment monitoring, assessment and management. However, its development is in a preliminary stage. With regard to the correlative scientific problem and approaches, specific researches are still limited. As viewed from criteria judgment, right nutrient control and estuarine ecosystem responses to nutrient, scientific basis for criteria development was analyzed. It is presented that reference condition can help to identify the state of criteria. Nitrogen, phosphorus, silicon and iron impose obvious limitation on phytoplankton growth, and they should be included in the control. Complex physical characteristics of estuaries result in different nutrient susceptibility, and geographical classification can contribute much to the practice. Resting on the above analysis and abroad experiences, methods for developing nutrient criteria in estuarine waters were put forward. Building up Regional Technical Assistance Group (RTAG), background investigation, estuary classification and partition, variables selection, data collection and in-situ observation, reference condition determination and criteria recommendation, and criteria evaluation and modification are the six main steps. Considered as the most vital one, estuary classification and partition as well as reference condition determination were particularly addressed. Several ways are available to achieve them while detailed selection and proper modulation should be applied to the process. In view of Chinese situation, establishing national estuarine database, developing national nutrient criteria manual, and setting up ecosystem-health-based estuarine nutrient criteria and standard system are highly suggested.