The Chihuahuan Desert, similar to many arid and semiarid ecosystems, has experienced dramatic changes in vegetation structure and ecosystem processes over the past 150 years. This “desertification” is manifested by the broad-scale expansion of unpalatable woody plants into perennial grasslands with associated loss of grasses and increase in soil degradation that compromise the ecosystem services provided to human populations. Given that nearly 40% of the Earth’s land surface and 20% of the world’s human population occur in regions susceptible to desertification, these changes are of substantial consequence. Although desertification has occurred globally over a similar time period, the explanations for this change are numerous and controversial. The overall goal of the Jornada Basin LTER program is to quantify the key factors and processes controlling ecosystem dynamics and patterns in Chihuahuan Desert landscapes in order to explain these variable responses. As part of our collaboration with the Jornada Experimental Range USDA-Agricultural Research Service, we have benefited from and contributed to a legacy of long-term research dating to 1915, and starting in 1982 with LTER. Our conceptual framework called “Landscape Linkages” integrates important, yet previously ignored or poorly understood processes, that provide insight into spatially and temporally variable dynamics. This framework includes five interacting components that connect patterns and processes across scales: (1) historical legacies, (2) environmental driving variables, (3) a soil-geomorphic template of patterns in local properties and their spatial context, and (4) multiple horizontal and vertical transport vectors (water, wind, animals) that (5) redistribute resources within and among spatial units. 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. We use a combination of experiments, long-term observations, simulation modeling, and remote sensing technologies to develop and test hypotheses related to this framework. Our research has resulted in knowledge and technologies that support the conservation and management of hundreds of millions of acres of land in North America and around the world.