Traditional monitoring approaches may have the objective of gathering data to estimate population size for a given species, but often lack the context of hypothesis testing. As such, many natural areas managers (responsible for ecological monitoring) and scientists have shared little common ground. The goal of monitoring should be to inform managers so that they can insure that the species, communities, and ecosystems under their charge are able to persist in the face of stressors, often from anthropogenic sources. The inherent complexity of natural systems makes this a daunting task, a task that requires a renewed partnership between managers and conservation biologists. The non-equilibrium paradigm of population dynamics establishes a theoretical framework for shifting monitoring objectives from only population estimates to understanding the processes that drive the dynamics of those populations. Using a hypothesis-driven scientific approach, monitoring designs can embrace the scientific method, provide insights into the ecological processes at work within natural systems, and importantly, point directly to if, when, and how active management may need to be employed in order to prevent the loss of biodiversity. This approach provides a common ground for conservation biologists and natural areas managers to forge partnerships to better understand the complexity of ecological systems and our ability to sustain those systems for future generations.