A pilot scale experiment for humic acid-enhanced remediation of diesel fuel, described in Part 1 of this series, is numerically simulated in three dimensions. Groundwater flow, enhanced solubilization of the diesel source, and reactive transport of the dissolved contaminants and humic acid carrier are solved with a finite element Galerkin approach. The model (BIONAPL) is calibrated by comparing observed and simulated concentrations of seven diesel fuel components (BTEX and methyl-, dimethyl- and trimethylnaphthalene) over a 1500-day monitoring period. Data from supporting bench scale tests were used to estimate contaminant-carrier binding coefficients and to simulate two-site sorption of the carrier to the aquifer sand. The model accurately reproduced the humic acid-induced 10-fold increase in apparent solubility of trimethylnaphthalene. Solubility increases on the order of 2-5 were simulated for methylnaphthalene and dimethylnaphthalene, respectively. Under the experimental and simulated conditions, the residual 500-ml diesel source was almost completely dissolved and degraded within 5 years. Without humic acid flushing, the simulations show complete source dissolution would take about six times longer.