Contemporary issues in agriculture and natural resource management (AGNR) span a wide spectrum of challenges and scales—from global climate change to resiliency in national and regional food systems to the sustainability of livelihoods of small-holder farmers—all of which may be characterized as complex problems. With rapid development of tools and technologies over the previous half century (e.g., computer simulation), a plethora of disciplines have developed methods to address individual components of these multifaceted, complex problems, oftentimes neglecting unintended consequences to other systems. A systems thinking approach is needed to (1) address these contemporary AGNR issues given their multi- and interdisciplinary aspects; (2) utilize a holistic perspective to accommodate all of the elements of the problem; and (3) include qualitative and quantitative techniques to incorporate “soft” and “hard” elements into the analyses. System dynamics (SD) methodology is uniquely suited to investigate AGNR given their inherently complex behaviors. In this paper, we review applications of SD to AGNR and discuss the potential contributions and roles of SD in addressing emergent problems of the 21st century. We identified numerous SD cases applied to water, soil, food systems, and smallholder issues. More importantly, several case studies are shown illustrating the tradeoffs between short-term and long-term strategies and the pitfalls of relying on quick fixes to AGNR problems (known as “fixes that backfire” and “shifting the burden”, well-known, commonly occurring, systemic structures—or archetypes—observed across numerous management situations [Senge, P.M. The Fifth Discipline
, 1st ed.; Doubleday: New York, NY, USA, 1990.]). We conclude that common attempts to alleviate AGNR problems, across continents and regardless of the type of resources involved, have suffered from reliance on short-term management strategies. To effectively address AGNR problems, longer-term thinking and strategies aimed at fundamental solutions will be needed to better identify and minimize the often delayed, and unintended, consequences arising from feedback between management interventions and AGNR systems.