Mung bean residues stimulate the hatching of soybean cyst nematode (SCN). In our previous study, combined incorporation of mung bean residues and biochar into soil can be effective in suppression of the soybean cyst nematode (SCN), Heterodera glycines, in the upper layer soil. However, there are no data available as to whether such effects are transmissible, and could for example be manifest in subsoil zones where such incorporation is confined to topsoils, via water-based pathways. We evaluated the effects of leachate passage from a biochar-amended soil in an upper soil zone to a lower zone in a microcosm-based system, upon a range of physicochemical properties and density of SCN. Disturbed soil was filled in a total of 9 cylindrical cores with two layers. The upper layer (0–15 cm) was amended with biochar at rates equivalent to 0, 0.3% or 1.8%, with bulk density set at of 1.1 g cm−3. The lower layer (15–25 cm) without biochar amendment was compacted to 1.2 g cm−3. Mung beans were grown for two weeks and incorporated into the upper layer. Water was surface-applied to the cores 4, 6, and 8 weeks after mung bean incorporation. After 16 weeks, the upper and lower layer soils were separately collected and assayed. The presence of biochar in the upper layer reduced the abundance of free-living nematodes, mainly bacterivorous, but increased that of a predator genus Ecumenicus in this zone. In the lower layer of soil under a biochar-amended upper layer, available P and soluble cations were increased as were abundances of total nematodes including Ecumenicus, resulting in greater maturity index, basal and structure indices. Notably, SCN density was decreased in lower zones by more than 90% compared to zero-biochar controls. This demonstrates that the effects of biochar upon soil properties, including impacts on biota and plant pathogens, are transmissible.