Transport and retention of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) were examined in water-saturated columns packed with three types of natural soils: a clay loam red soil (RS), a sandy loam fluvo-aquic soil (FS), and a loam huangni soil (HS). Specific factors investigated included monovalent K+ and divalent Ca2+ concentrations and the coupled effect of Ca2+ with humic acid (HA) at a PVP-AgNP concentration of 10 mg L−1 and Darcy velocity of 0.182 cm min−1. Our results showed that transport of PVP-AgNPs decreased with increasing K+ and Ca2+ concentrations, primarily due to enhanced aggregation of PVP-AgNPs and reduced repulsive interactions between PVP-AgNPs and soil grains. Consistent with the Derjaguin–Landau–Verwey–Overbeek theory, retention of PVP-AgNPs was more pronounced in the presence of Ca2+ than K+. However, the presence of HA significantly weakened the mobility of PVP-AgNPs with increasing Ca2+ concentration, probably due to increased aggregation of PVP-AgNPs (forming a HA–Ca–PVP-AgNPs complex). Irrespective of solution chemistry, the mobility of PVP-AgNPs in all three soils remained in the order of RS < FS < HS. Principal components analysis indicated that the mobility of PVP-AgNPs was positively correlated with pH, cation exchange capacity, and soil organic matter content and was negatively correlated with Fe oxide content and specific surface area of the soils. Overall, our findings highlight the dominant role of soil physicochemical properties in the mobility of Ag nanoparticles in natural soils and the importance of investigating these factors to better understand the fate of engineered nanoparticles in natural environments at the point of disposal and protecting groundwater resources.