This study evaluated the effect of 13 years of swine-manure application on the changes in soil hydraulic properties, and as associated physicochemical properties, with a focus on heavy metal mobility. Various soil hydraulic properties were measured, including soil water retention (SWR), saturated field hydraulic conductivity (Kfs) and unsaturated field hydraulic conductivity (Kfunsat) using a disc infiltrometer. Heavy metal mobility was evaluated with a sequential extraction procedure. At 0–30 cm soil depth in the heavily manured plot (SMhigh plot), SWR at 0 to −100 kPa was significantly larger than in plots amended with a standard amount of manure (SMstd plot) or with chemical fertilizer (CF plot). Kfs and Kfunsat values in both manure-amended plots were less than in the CF plot under dry soil conditions but greater than those of the CF plot under wet soil conditions. Furthermore, Kfs and Kfunsat did not necessarily increase with manure application rates. On the other hand, high-mobility metal fractions, such as the exchangeable fraction of Zn, and the CH3CO2Na-extractable fraction of Zn and Mn, and the metal–organic complex fractions of Zn, Cu and Mn, increased with the greater manure application rate. In addition, low-mobility metal fractions, the organically bound fractions of Zn, Cu and Mn in the high SM plot and the easily reducible metal oxide fraction of Mn in both manure-amended plots were probably affected and released into high-mobility fractions. This indicated that manure application changed the soil redox conditions by improving the soil structure, depending on the water content of soil pores. Despite the reduction of Kfs and Kfunsat by heavy manure application, the transport of high-mobility metal fractions with either surface water flow or infiltration water flow could be controlled by soil water content at the beginning of a rain or irrigation event.