The effect of topographic characteristics of land uses on stream water quality must be addressed for a better understanding of the complex relationship between land use and stream water quality. In this study, Geographic Information System (GIS) and Pearson correlation analysis were used to determine whether there were relationship between land use types and stream water quality at the sub-basin scale in the Wei River basin, China, during the dry and rainy seasons in 2012. Temporal variation of these relations was observed, indicating that the relationships between water quality variables and different land uses were weaker in rainy seasons than that in dry seasons. Compared with other land uses, agriculture and urban lands had a stronger relationship with water quality variables in both rainy and dry seasons. Topographic characteristics of land use were employed to further analyze these relationships. The results showed that seasonal variation also occurred in the complex relationship, and land uses in steeper slopes generally had a stronger influence on stream water quality than those in flatter ones. For the riparian zone of each sampling site, the slope coefficients were weaker than those at the sub-basin scale. Land use type near stream water was generally a better indicator for the effectiveness of water quality. These results suggest that the slope and proximity should be taken into account for better land use management.