Anthropogenic activity is causing dramatic changes in the nitrogen (N) cycle in many ecosystems. Most research has focused on the increase in N input caused by atmospheric deposition and invasion of N-fixing species, and on their effects on resource availability and species composition. However, in contrast to many ecosystems experiencing large increases in N input, many arid ecosystems are experiencing loss of nutrients due to land-use change. An important component of many arid ecosystems on a worldwide basis is the microbiotic crust, a biological soil crust composed of lichens, cyanobacteria, mosses, and algae. Nitrogen fixation by lichens and cyanobacteria comprising the crust is the primary source of N input in many of these ecosystems. We quantified the long-term consequences of surface disturbance in an arid ecosystem on the Colorado Plateau by comparing pristine sites with those of known disturbance history. Disturbance caused an increase in the abundance of cyanobacteria and a decrease in lichens within the microbiotic crust. Carbon isotope composition (δ13C) of the crust reflects this shift in species composition; values for disturbed sites were 4.5‰ higher than undisturbed sites. Nitrogen isotope composition (δ15N) of the microbiotic crust was 1.5–2.2‰ higher for disturbed sites, probably resulting from relatively greater gaseous N loss from the crust. Historic disturbance has caused a long-term decrease in rates of N fixation by the microbiotic crust; nitrogenase activity in pristine sites was 250% greater than sites intermittently disturbed 30 yr ago. The decrease in N input from fixation and continued gaseous N loss has caused a 25–75% decrease in soil N content. Altering relative rates of N input and loss, coupled with input of N from microbiotic crusts with relatively higher δ15N, has caused an increase in soil and plant δ15N at disturbed sites. This decrease in soil N caused by disturbance will likely cause changes in species composition similar to those observed in ecosystems that have been disrupted by excess N input from atmospheric deposition.