In recent years, perfluoroalkyl acids (PFAAs) have become ubiquitously distributed in water environments, especially in riverine waters receiving effluents from wastewater treatment plants (WWTPs) in urban areas. With rapid economic development, China has become the main market of manufacturing and consuming fluorinated products. While studies concerning PFAAs on dimension of urban water system are scarce. To elucidate the distribution patterns of PFAAs using multi-matrices, the effects of spatial-temporal factors on the partition behaviors of PFAAs were investigated in different riverine environments in the downtown area of Nanjing, East China. Predominated by perfluorooctanoic acid (PFOA), sum PFAAs (∑PFAAs) in the water phase were with concentrations of 0.8˜274.6 ng/L, characteristically higher in the dry season and lower in the wet season. The composition profiles in sediments (∑PFAAs 0.8˜11.4 ng/g dry weight) differed from that in water, being with a larger proportion of longer-chain PFAAs. The main sources of PFAAs in water were identified as industrial discharge, uncontrolled sewage discharge or WWTP effluents, surface runoff and nonpoint sources. The discharge fluxes of ∑PFAAs from Nanjing City can reach at 916.5 g/d for the Qinhuai River and 134.1 g/d for WWTPs along the Yangtze River. Fish have been shown to accumulate PFAAs in various tissues, with bioaccumulation positively correlated with perfluoroalkyl chain length. The hazard indexes associated with consumption of river fish were estimated low for Nanjing local population.