The spatiotemporal characteristics of river water quality are the key indicators for ecosystem health evaluation in basins. Land use patterns, as one of the main driving forces of water quality change, affect stream water quality differently with the variations in the spatiotemporal scales. Thus, quantitative analysis of the relationship between different land cover types and river water quality contributes to a better understanding of the effects of land cover on water quality, the landscape planning of water quality protection, and integrated water resources management. Based on water quality data of 2006–2018 at 18 typical water quality stations in the Yangtze River basin, this study analyzed the spatial and temporal variation characteristics of water quality by using the single-factor water quality identification index through statistical analysis. Furthermore, the Spearman correlation analysis method was adopted to quantify the spatial-scale and temporal-scale effects of various land uses, including agricultural land (AL), forest land (FL), grassland (GL), water area (WA), and construction land (CL), on the stream water quality of dissolved oxygen (DO), chemical oxygen demand (CODMn), and ammonia (NH3-N). The results showed that (1) in terms of temporal variation, the water quality of the river has improved significantly and the tributaries have improved more than the main rivers; (2) in the spatial variation respect, the water quality pollutants in the tributaries are significantly higher than those in the main stream, and the concentration of pollutants increases with the decrease of the distance from the estuary; and (3) the correlation between DO and land use is low, while that between NH3-N, CODMn, and land use is high. CL and AL have a negative effect on water quality, while FL and GL have a purifying effect on water quality. In particular, AL and CL have a significant positive correlation with pollutants in water. Compared with NH3-N, CODMn has a higher correlation with land use at a larger scale. The results highlight the spatial scale and seasonal dependence of land use on water quality, which can provide a scientific basis for land management and seasonal pollution control.