In the current context of urbanization and climate change, anthropogenic activities have changed land use and land cover, which seriously affect water quality and riverine ecosystems. The impact of land use changes on water quality has great temporal and spatial heterogeneity. Here, we studied the relationships between water quality and landscape characteristics of the Houxi River watershed covering 74% of surface area of the Jimei district in Xiamen City. We analyzed spatial and temporal changes in the water quality from 2013 to 2017 in both dry and wet seasons. Our results showed obvious spatial heterogeneity from the upstream to downstream in water quality. Dissolved oxygen (DO) in the Houxi River upstream and downstream river sections met categories Ⅱ and Ⅴ of surface water quality standards (GB3838-2002), respectively, whereas total nitrogen (TN) and total phosphorus (TP) exceeded the national standards in most cases. Shidou and Bantou reservoirs in the upstream of the watershed were mainly in the range of light to middle eutrophic conditions during the study period. The percent of forest land was higher than 70% in the upstream watershed, which could significantly protect water quality. The proportion of built land and cropland associated with patch density (PD), Shannon's diversity index (SHDI), and location-weighted landscape index (LWLI) increased from the upstream to downstream, leading to increasing concentrations of TN, TP, and Chl a. Statistical analyses, including correlation analysis, regression analysis, redundancy analysis, and a structural equation model showed that, cropland and built land were the dominant land use types that could potentially affect water quality in complex ways. The relationships were also strong between the landscape index and DO, TN, TP, and Chl-a. The RDA results explained 78.6% and 74.0% in water quality variation in the dry and wet seasons, respectively. The influence of landscape characteristics on TN and TP, and its influence on Chl a was more pronounced in the wet and dry seasons, respectively. Overall, our results showed that the land use patterns, patch density, relative distance, elevation, and slope degree had a great impact on water quality in the watershed. Therefore, it is necessary to adopt appropriate land use management strategies in the watershed, particularly by controlling the runoff linked with agriculture and urbanization.