Recently, systematical studies on aquatic ecoregion zoning have been launched in several representative basins in China. Both theory and application of aquatic ecoregion zoning at watershed scale are involved, which is toward a framework including an integrated indicators system for ecoregion zoning. National ecoregion zoning based on aquatic ecosystem function is the basis of water environment management in China. Theorization of driving mechanism, standardization of indicators and quantification of zoning technique are key issues to be solved for the national ecoregion zoning. On the basis of previous studies, a framework comprising of a series of indicators and a technique for aquatic ecoregion is proposed, and potential problems are analyzed as well. The framework includes: (i) selection of indicators, (ii) the mechanism demonstrating the impact of environmental factors on aquatic ecosystem, and (iii) an operational technique for ecoregion zoning. The indicators including environmental and aquatic elements are the basis of the framework. The indicators system is expressed as two layers: data and application. The former is comprised of sample and monitoring data for environmental and aquatic factors, while the latter united the data for universal application in ecoregion zoning by standardization approaches. Data is selected by some statistical methods such as Canonical Correspondence Analysis (CCA) and Principal Components Analysis (PCA). The indicator system is proposed based on previous studies but is unintentional to be the final ecoregion indicators. Future studies and practices on ecoregion zoning may modify those indicators. The mechanism provides scientific supports for the framework, which is described by an aqua-terrestrial ecohydrological model covering hydrological and ecological processes based on hydrological models. The aqua-terrestrial ecohydrological model reflects the environmental influences on aquatic ecosystem and expresses them in statistical or physical manner. The operational technique makes it possible to perform the zoning. This technique combines the “top-down” and “bottom-up” approaches. The former is mainly applied at large scales while the latter is applied at subecoregions and inferior. The “bottom-up” approach is performed based on the delineation of subbasins (catchments), which is considered as a unit for subecoregion zoning that involves all aquatic and terrestrial components. Statistically significant difference in defined ecoregion indicators between two subbasins is examined and non-significant different subbasins will be merged. This procedure processes until no significant differences are detected. The combination of two approaches may facilitate the operation of zoning and reduce influence of subjective factors. The framework is supposed to facilitate and ensure the practice of the national ecoregion zoning. The issue of scale is also discussed. The scale of aquatic ecosystem should be represented in the indicator system. Though the size of watershed is not a scale for ecoregion, discussion is still based on watershed in this paper since there are no general acknowledged sizes for ranked ecoregions. However, further investigation and practices are needed to test and examine the framework proposed in this study. The objective of this study is to provide some references and theoretic support for the on-going aquatic ecoregion zoning in China. Those practices may further improve and even modify the framework proposed in this study.