Water quality deterioration has become a severe environmental problem across the world and has been an urgent concern for the public and government authorities. Non-point source (NPS) pollution caused by land use is recognized as one of the most important impacts on water quality; and agricultural land use is a major source leading to eutrophication. NPS pollutants transfer along river hierarchies and enter lakes/seas eventually. Hydrological processes and ecological characteristics usually vary by river hierarchy, as a result, water quality and land use could manifest various interactions, depending on level of river hierarchies and spatial scale of observation. Using monitoring data of water quality in 2006-2007 and contemporary Landsat TM images, we investigated the responses of water quality to riparian land uses, with respect to main streams vs. branches in Guan River Basin, north Jiangsu Province, China. Multiple linear regression models were used to examine the relationships at the scales ranging from 0.0 to 0.5 km in width and 0.0-10.0 km in length along the river channels. We found higher nutrient concentrations but lower organic pollutant concentrations in the branches than the main streams. The main streams showed significantly better water quality than the branches in dry seasons; while their difference was small in wet seasons. With fixed buffering widths, water quality of the main streams had significant correlations with land use only at relatively small (i.e. 0.0-4.0 km) buffering lengths; while for the branches, the correlations were significant at all buffering lengths. With fixed buffering length, the largest variance in water quality was explained by the land use within 0.3 km of the river channels for all the main streams and branches. The concentrations of TN (Total Nitrogen) and TP (Total Phosphorus) were related to land use mostly on larger scales, while such relation was observed only on smaller scales for organic pollutants. The result indicated that it is necessary to study the correlations between land use and water quality in each river system hierarchy, respectively, at appropriate scales.