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Due to tightly coupled physical, chemical, and biological processes that often behave in nonlinear, counterintuitive ways, it is argued that soil is an archetype of a complex system. Unfortunately, human intuition and decision making has been shown to be inadequate when dealing with complex systems. This poses significant challenges for managers or policy makers responding to environmental externalities where soil dynamics play a central role (e.g., biogeochemical cycles) and where full ranges of outcomes result from numerous feedback processes not easily captured by reductionist approaches. In order to improve interpretation of these soil feedbacks, a dynamic systems framework is outlined (capturing feedback often excluded from investigation or left to intuition) and then applied to agroecosystem management problems related to irrigation or tillage practices that drive nutrient cycling (e.g., soil water, nitrogen, carbon, and sodium). Key soil feedbacks are captured via a variety of previously developed models simulating soil processes and their interactions. Results indicated that soil system trade-offs arising from conservation adoption (drip irrigation or no-tillage) provided reasonable supporting evidence (via compensating feedbacks) to managers justifying slow adoption of conservation practices. Modeling soils on the foundation provided in the complex systems sciences remains an area for innovations useful for improving soil system management