Urbanization has caused severe negative impacts on intra-urban river water bodies. In this paper, 22 physicochemical parameters were measured at 20 locations in the level period and 29 locations in the wet and dry period using nearby urban area surface water samples from a medium-sized polluted river (a lake-river continuum, i.e., Xunsi River, Qingling River and Tangxun Lake) in the Yangtze River watershed in Wuhan, China. In this study, the environmental quality standards for surface water of China (GB3838-2002) and the WHO drinking water standard (2011) were used as reference standards. After the basic physicochemical parameters were evaluated, the possible sources of pollution in the study area under urban pressure were examined by applying multivariate statistical techniques. The factor analysis method and entropy weighting method identified three critical factors describing the type of surface water pollution in the watershed: (1) pollution from nutrients, mainly nitrogen pollution, (2) trace metals pollution, mainly from Fe and Pb, and (3) organic pollution. Based on multivariate analysis, the weighted arithmetic water quality index (WQI) was used to assess the water quality of each period. The WQI results show that the water near the urban area of the watershed temporally shows light to moderate pollution overall in the level and wet periods, and sever pollution in the dry period. The worst water quality indicating water that is not suitable for any practical use occurs in the dry period. Spatially distributed in clusters and strips visualized in kriging method, the water quality of the lake source and upstream is better than that of the downstream. In addition, Escherichia coli was detected at consistently high levels, and although the river is not a source of drinking water, it could pose a threat to downstream waterworks.