Contamination of agricultural soil by heavy metals has become a global issue concerning food security and human health risk. In this study, a soil investigation was conducted to evaluate metals accumulation, potential ecological and health risks as well as to identify sources of metals in paddy soils in Hanzhong City, which is located in a sedimentary basin. Ninety-two (92) surface soil samples (bulk soil) and their corresponding rice samples, 21 irrigation water samples, and 18 fertilizer samples were collected from two typical counties and quantified for the heavy metals (i.e., As, Cd, Cu, Hg, Pb, and Zn) concentrations. The results showed that As, Cd, and Zn were the main contaminants in soils in the studied area. Additionally, elevated Hg content in soils might also pose risks to the local ecosystem. Cadmium and As demonstrated high mobility, and their average contents in rice grains were slightly higher than the permissible threshold (0.20 mg kg−1). Moreover, Pb, As, and Cd intake via rice consumption might result in potential risks to local residents. Metal distribution revealed that pollution in the studied area is non-homogeneous, and agricultural activities (As, Cu, and Cd), transportation emission (Cu and Pb), coal combustion (Hg and As), and smelting activities (Zn, Pb, and Cu) were ascertained as the potential sources based on the Positive matrix factorization (PMF) analysis results. Display omitted •Metal contents in 92 soil and rice, 22 water, and 18 fertilizer samples were determined.•Cd and As were the main pollutants in soils, and soil Hg may pose risks to local ecosystem.•Average Cd and As contents in rice grains slightly exceeded the permissive limits.•Daily intake of Pb, As, and Cd might pose risks to local residents health.•Five sources were identified as main contributors to the elevated metals in paddy soils.