This research investigated the removal of heavy metal ions (Cd, Cu, Pb, and Zn) and metalloid (As) common to stormwater runoff onto biochar-based media arranged in multiple configurations. Laboratory scale column experiments were conducted to quantify heavy metal removal efficiencies using sand, biochar, and nZVI-modified biochar (BC-nZVI) in four media configurations: a homogeneous mixture of sand and biochar (BCM); biochar layered in sand (BCL); BC-nZVI layered in sand (BCZ); and sand as a control. An inverse modeling approach was implemented to measured moisture and experimental data to determine media hydraulic parameters (θr, θs, α, n and Ks) and adsorption coefficients. The experiment was conducted using laboratory synthesized stormwater over 200 days at a rate of 5 cm/day. BCZ exhibited an excellent removal (99%) of As due to the high attachment to nZVI, via surface complexations. Biochar with abundant surface oxygen functional groups exhibited a great (99%) removal of Cd and Zn in both BCL and BCM columns. Water contents were observed 66.0, 44.3, 41.4, and 7.2% for BCL, BCM, BCZ, and sand, respectively. The attachment coefficients varied from 21.5 to 44.9, 16.1 to 19.3, 18.8 to 26.0, and 9.6 to 19.9 L/kg for BCL, BCM, BCZ, and sand, respectively. This study’s output provides useful information for stormwater management practices.