The Mianyang section of the Fujiang River is Mianyang City’s main source of drinking water; therefore, we must ascertain this aquatic ecosystem’s heavy metal(loid)s (HMs) pollution status to protect the health of local residents. We examined 27 surface sediment samples using X-ray fluorescence spectrometry for 10 widely concerned HMs. We applied spatial interpolation, the positive matrix factorization, and a potential ecological risk index to determine the spatial distribution, source, and potential ecological risk of HMs in the sediment, respectively. Our results showed that Mn, Co, Cr, As, Zn, and Pb were disturbed by human activities. The levels of HM content at different sites were different due to the influence of urban human activities. Our source apportionment results showed that As, Cu, Pb, and Mn principally originated from mixed sources of industry and traffic; Ba and Co were chiefly derived from architectural sources; Ni, Zn, and V were mainly from natural sources; and Cr originated from industrial sources. Mixed, architectural, natural, and industrial sources account for 25.62%, 25.93%, 24.52%, and 23.93% of the total HM content, respectively. The HMs were of low ecological risk, which were mainly caused by As and Co. In our study, the mixed source was the priority anthropogenic source, and As and Co were the priority elements for further risk control in the Mianyang section of the Fujiang River.