A vegetable production base, typical of the area along the Yangtze River in Nanjing, was selected as a case for study. Concentrations of heavy metals in topsoil, soil profiles, fertilizers and atmospheric deposition were measured for analysis of spatial variation of soil heavy metal anomaly and sources of the heavy metals in the soils. Results show that (1) the average content of cadmium (Cd), arsenic (As), mercury (Hg), lead (Pb), copper (Cu), zinc (Zn) and chromium (Cr) in topsoil was 0.33, 11.2, 0.09, 36.2, 45.4, 120 and 98.7 mg kg^-1, respectively, all higher than their respective soil background value in Nanjing; Concentrations of Cd in 49% of the soil samples were found to be above the criteria of GradeⅡof the Standard for Soil Environmental Quality of China, implying higher Cd accumulations in the soils. (2) The concentrations of heavy metals in the topsoils were closely related to soil pH, soil organic matter and soil textures of the area; Spatial distribution of the heavy metals in topsoil, except Cr, was characterized by a trend of tending to be higher in the southeast and lower in the northwest, which was consistent with the spatial distribution of soil organic matter and opposite to the spatial distribution of soil pH; Concentrations of the heavy metals were higher in silty clay soils than in silty clay loam and silty loam soils. (3) Accumulation and distribution of the heavy metals in the soils was also related to the terrain, the layout of agriculture and industry, and the perennial dominant wind direction in the study area. The maximum values of Cd, Cu and Zn contents were found in the southeast of the study area and the maximum values of As in the centre. Concentrations of Hg tended to be high in areas with intensive agriculture and peaked in the northeast of the study area, while the highest concentration of Pb was found in the northwest and southeast of the study area. (4) In addition to the natural geological background, agricultural fertilization and atmospheric deposition were also important contributors to heavy metals accumulation in the soils of the area. In terms of concentrations of Cd in fertilizers, a decreasing order was found of commodity chemical fertilizer > organic fertilizer > manure > rapeseed cake. Contents of Cd, As and Hg were higher in chemical fertilizer, while contents of Pb and Cr higher in organic fertilizer. The contents of Cu and Zn in organic fertilizer were much higher than those in the other fertilizers, which were mainly related to the higher concentrations of Cu and Zn in the feed of livestock. As heavy metals in the soil has the feature of long-term accumulation, long-term intensive application of fertilizers high in heavy metals would lead to heavy metal accumulation in the soil, with a risk of gradually exceeding the standard for soil environmental quality or environmental capacity. The content of Cr in the atmospheric deposition was approximate to the background value of the soil in Nanjing. Compared with other researches on atmospheric deposition in Nanjing, this study found higher contents of Cu and Zn, which is probably because some of the sampling sites were quite close to industry parks in the vicinity and hence affected by chemical activities of the plants. Atmospheric deposition flux varied sharply from month to month, and contents of heavy metals increased obviously in winter, especially in the northwest industrial area. Contents of Pb and Cu in the atmospheric deposition varied in a similar way. Thus, it could be inferred that they have similar sources in the study area.