Technical Abstract: Process-level whole-farm simulation provides a tool for evaluating the potential impacts of alternative production strategies without cost or risk to the producer. When the performance of simulated systems is supported through field measurements, a more accurate assessment is obtained. The Integrated Farm System Model was able to represent the corn silage production, water balance, volatile ammonia nitrogen (N) loss, nitrate N leaching loss, and phosphorus (P) runoff loss measured in field plots with manure application treatments of no manure application, broadcast application without incorporation, broadcast application with tillage incorporation, band application with aeration, shallow disk injection, and high pressure injection. Measured and simulated results showed that incorporation of manure below the soil surface through tillage or injection reduced ammonia loss but tended to increase nitrate leaching loss. Effects of the manure application strategy on P losses were less clear, but there was a trend toward less runoff of soluble P with subsurface injection and greater loss of sediment-bound P when tillage was used to incorporate manure. Whole-farm simulations of each of the manure application strategies on a representative dairy farm in Pennsylvania indicate that reductions in ammonia N loss and P runoff can be obtained with the use of shallow disk injection without adversely affecting farm profitability. Use of the other incorporation methods caused a small reduction in farm profit compared to broadcast application without incorporation. Additional benefits such as odor reduction may also be obtained, which may help justify the additional production cost even when no direct economic benefit is received.