Purpose The Yellow River Delta, an active land-ocean interaction area, will develop into a large eco-economic region in East China during the coming decade. It is necessary to assess the geochemical features of heavy metals in the soils. The objectives of this research were to evaluate the concentrations and distribution of heavy metals (Cr, Ni, Cu, Zn, Pb, and Cd) in soil profiles of the area and to identify their sources. Materials and methods Horizon samples were collected based on pedogenic features from bottom to top in each profile to a depth of 120 cm and a total of 92 samples were collected. The sampling sites were grouped into four lines from inland to coastal area with three land use types (cotton field, cereal field, and wetland). The concentrations of Cr, Ni, Cu, Zn, Pb, and Cd were measured by inductively coupled plasma-mass spectrometry. Iron oxide fractions in the soil were extracted by oxalate-oxalic acid and dithionite-citrate-bicarbonate. X-ray diffraction (XRD) was used to determine the mineral composition of the soils. Multivariate statistical analysis and historical data were employed to identify the possible sources of these heavy metals.Results and discussion The mean concentrations of heavy metals were elevated along the Yellow River region and in the southern part of the delta; however, they were generally lower than the Chinese guideline values. As for the depth distribution of heavy metals in soil profiles, the maximum values of Cr, Ni, Cu, Zn, and Cd in middle horizon of cotton field were almost twice than those in surface horizon. The iron oxides and XRD analysis indicated that the trace elements accumulation appeared to be related with the contents of crystalline iron oxide and layer silicates. Historical data from suspended sediments of the Yellow River and principal component analysis (PCA) implied that most of the metals (Cr, Ni, Cu, and Zn) were sourced from natural alluviation and sedimentation. Conclusions The Yellow River Delta soils were slightly polluted by heavy metals the Yellow River Delta. The special pedogenic horizon characterized by higher iron oxides and layered silicates minerals in the middle and lower part of the soil profile was found with heavy metals enrichment, which required to be studied further. Suspended sediments transported by the Yellow River were suggested to be one of the major sources for the heavy metals accumulation in the basal soils of this region.