The Critical Zone (CZ) includes the biophysical processes occurring from the top of the vegetation canopy to the weathering zone below the groundwater table. CZ services provide a measure for the goods and benefits derived from CZ processes. In intensively managed landscapes, cropland is altered through anthropogenic energy inputs to derive more productivity, as agricultural products, than would be possible under natural conditions. However, the actual costs of alterations to CZ functions within landscape profiles are unknown. Through comparisons of corn feed and corn-based ethanol, we show that valuation of these CZ services in monetary terms provides a more concrete tool for characterizing seemingly abstract environmental damages from agricultural production systems. Multiple models are combined to simulate the movement of nutrients throughout the soil system, enabling the measurement of agricultural anthropogenic impacts to the CZ’s regulating services. Results indicate water quality and atmospheric stabilizing services, measured by soil carbon storage, carbon respiration, and nitrate leaching, among others, can cost more than double that of emissions estimated in previous studies. Energy efficiency in addition to environmental impact is assessed to demonstrate how the inclusion of CZ services is necessary in accounting for the entire life cycle of agricultural production systems. These results conclude that feed production systems are more energy efficient and less environmentally costly than corn-based ethanol.