Although desertification is a global phenomenon and numerous studies have provided information on dynamics at specific sites, spatial and temporal variations in response to desertification have led to alternative, and often controversial, hypotheses about the key factors that determine these dynamics. We present a new research framework that includes five interacting elements to explain these variable dynamics: (1) historical legacies, (2) environmental driving variables, (3) a soil-geomorphic template of patterns in local properties and their spatial context, (4) multiple horizontal and vertical transport vectors (water, wind, animals), and (5) redistribution of resources within and among spatial units by the transport vectors, in interaction with other drivers. Interactions and feedbacks among these elements within and across spatial scales generate threshold changes in pattern and dynamics that can result in alternative future states, from grasslands to shrublands, and a reorganization of the landscape. We offer a six-step operational approach that is applicable to many complex landscapes, and illustrate its utility for understanding present-day landscape organization, forecasting future dynamics, and making more effective management decisions.