Liquid swine manure has nitrogen and phosphorus that can be utilized for crop fertilization, but due to high levels of application the manure will often flow through macropores. If the manure reaches the water table it can pose an environmental risk. The permeation can be slowed by low permeability skin layers in the macropores, compact soil crusts, low permeability plowpan layers, or a tile drainage system. As well, the percent of dry matter in the liquid manure will affect viscosity, with a 5% increase in dry matter increasing viscosity by one order of magnitude. This study’s goal was to modify a dual-permeability model and apply it in field, determine the sensitivity of tile drain discharge rates, and numerically assess nutrient residue with additional variabilities. The dual-permeability model was able to give a fairly accurate prediction of liquid manure movement. The modified model included application method (injected or surface banded), the effect of soil crust and plowpan layers, and the anisotrophy ratios for the macropores. Viscosity was important to manure flow rates, and increasing viscosity of manure should be considered to slow permeation. Movement depends on soil features: a solid crust will slow movement, but a plowpan layer with vertical macropores will increase it. Flow has temporal variability, and the leading or trailing edges will be influenced differently by the soil properties. Overall, it is important to understand how the combination of specific soil characteristics influence liquid manure movement, and the dual-permeability model is a effective model to do so.