A scarcity of information exists on how physical processes govern the movement of liquid manure, or other viscous fluids, through layered macroporous soils. To elucidate these complex flow and transport phenomena, a viscosity dependent, two-dimensional dual-permeability model that considers macropore anisotropy is employed to simulate field experiments where liquid swine manure (LSM) was applied to silt loam with both a soil crust and plowpan layer present. Using data from the field experiment as a benchmark, the model was used to predict nutrient (NH4-N and total P) breakthrough to tile drains; and to assess the influence of reduced permeability crust and plowpan layers, and fluid viscosity, on solute movement within 48 h of LSM application. Results demonstrate the importance of viscosity on flow and transport in macroporous soils. By increasing LSM viscosity, nutrient breakthrough to tile drains can be greatly reduced, and near surface nutrient retention can increase. The presence of a nonmacroporous soil crust layer can also lead to reduced nutrient concentrations in tile discharge by reducing pressure heads in the underlying A-horizon soil matrix, resulting in reduced macropore flow; whereas a low permeability plowpan layer at the base of the A horizon can increase pressure heads in the A-horizon soil matrix and lead to increased macropore flow. Multiple target point parameter sensitivity analysis revealed that relative parameter sensitivity can be a transient characteristic, and that hydraulic properties of the A and B horizon tend to exhibit their greatest influence over the respective early and late time solute breakthrough characteristics.