The relationship between land landscape and water quality has been a hot topic, especially for researchers in headwater catchment, because of drinking water safety and ecological protection. In this study, Lita Watershed, a typical headwater catchment of Southeast China, was selected as the study area. During 2015 and 2016, water samples were collected from 18 sampling points every month, and 19 water quality parameters were tested such as nutrients and heavy metals. Through multistatistics analysis, the results show that the most sensitive water quality parameters are Cr, NO3, NO2, and COD. The type and scale of water body have direct effects on water quality, while the land-use patterns in the surrounding areas have an indirect impact on the concentration and migration of pollutants. This effect is sensitive to seasonal change because heavy metals are mainly from atmospheric deposition, but nutrients are mainly from agricultural nonpoint source pollution. According to the results, increasing the proportion of forest land and paddy field is effective to the reduction of water nutrients. Besides, balancing the configuration of water bodies, especially increasing the capacity of the pond, can significantly alleviate the water pollution in the dry season. This study is useful to provide policy suggestion for refined watershed management and water source planning basing on seasons and pollution sources.