Rural revitalization denotes the gathering of large populations in rural areas and the subsequent gradual urbanization. Rural environments have been deteriorated by heavy metals (HMs) over the last few years. Without the existence of large-scale industries, the accumulation of HMs in sediments due to population aggregation in rural environments needs to be scientifically confirmed. Therefore, in this study we first understand the sediment pollution in rural environments in China and across the globe, and subsequently investigate HMs in sediments in rural micro water. The study area, Sichuan Province, China, was divided into two areas, namely, sparsely populated areas (SPA) and densely populated areas (DPA). Eight typical HMs (As, Zn, Ni, Hg, Cd, Cr, Cu, and Pb) were selected to target in riverine sediments, and the content and spatial distribution characteristics were analyzed. The results indicate that As, Hg, Cd, and Pb concentrations in sediments were higher than background values (BVs), with high concentration sample sites located in the DPA. In addition, the geo-accumulation index (Igeo), pollution load index (PLI) and potential ecological risk index (RI) were used to quantitatively evaluate the pollution characteristics of HMs in sediments, revealing that the sediments exhibited high As and Hg pollution in the DPA (PLI = 1.09). In general, mild (RI = 48.76) and moderate (RI = 154.92) HM pollution was observed in the sediments of the SPA and DPA, respectively, based on the high PLI (> 1.0) and RI (> 150) values. Correlation analysis and principal component analysis (PCA) indicate that the Cd in the sediment generally originated from geogenic sources, while the other elements (Zn, As, Cu, Cr, Hg, Ni and Pb) were primarily linked to anthropogenic sources. Finally, the results demonstrate that population aggregation will lead to the enrichment of HMs.