Aquatic ecoregion is the basis for the management of watershed environment in China. Indicators for ecoregion zoning are important for the framework of aquatic ecoregion framework. Several indicators for ecoregion zoning have been proposed in the previous studies. However, most of those indicators lack theoretical basis. For example, how to determine the characteristic scales of environmental factors and link it to a given level ecoregion are not investigated thoroughly. In order to address this issue, scale analysis on topography (DEM and slope) and vegetation is made by using scale variance analysis (SV) method, and precipitation data by the scale covariance methods (SC). Scale variance analysis is a method to detect spatial scales where significant spatial heterogeneity exists for raster data. Boxes are selected for scale variance analysis with the size of 2×2, 4×2, 4×4, 8×4, 8×8, 16×8, 16×16, 32×16, 32×32, 64×32, 64×64, 128×64, 128×128, 256×128, 256×256, 530×256. Scale covariance method is deliberately proposed for long term point-measured records (e.g. precipitation), which cannot be appropriately analyzed with the scale variance method. SC method calculates covariance and correlation coefficient for each pair of point-measured records. Distance between every two points is estimated and then the pairs with distance less than predefined scales are selected for SC calculation. Largest outside rectangle of the boundary in the Liao River basin is chosen for data extraction and analysis. Altitude and slope derived from the SRTM-DEM data in the Liao River basin, provided by USGS, is utilized for scale variance analysis. NDVI in the Liao River basin in 2007 is selected for vegetation scale variance analysis. Both DEM and NDVI data are resampled with the cell size of 1km × 1km. Precipitation data from 34 stations within and around the Liao River basin from 1957 to 2008 are collected for scale covariance analysis. Scale covariance analysis results indicate that precipitation shows a characteristic scale of 75 km, corresponding to a box size of 5625 km², and scale variance analysis shows that both topography (DEM and slope) and vegetation (NDVI) have characteristic scales of 16 km, 32 km, 64 km, and 128 km, corresponding to box sizes of 156 km², 1024 km², 16384 km², respectively. Referring to the National Ecological Unit Hierarchy (NEUH) in USA, the aquatic ecoregion framework by US-EPA, and ecoregions defined in the European Water Framework Directive, the range of aquatic ecoregion in China is preliminarily determined. Size of aquatic ecoregion level Ⅰ is supposed to be more than 5000 km² and less than 50000 km², which approximately corresponds to the ecoregions between the levels of "Province" and "Section" in the NEUH or the very large ecoregions in the WFD, and the size for aquatic ecoregion level Ⅱ is about 1000 to 5000 km², which approximately corresponds to the ecoregions of level "Subsection" in the NEUH or the large ecoregion in the WFD. On the basis of the primarily defined extent of both aquatic ecoregion level Ⅰ and level Ⅱ, potential indicators for level Ⅰ and level Ⅱ ecoregions are discussed. Conclusions are important for the selection of indicators in aquatic ecoregion zoning.