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Native annual plant species constitute a large proportion of the plant diversity found in arid vegetation types within the southwestern United States; yet, little is known about controls on diversity patterns along natural and anthropogenic gradients. In this study we evaluated native species richness and exotic species cover across overlapping gradients of precipitation, wind, and N deposition in the Colorado Desert of southern California. Factors allowing native diversity to persist under high N deposition and high wind were also evaluated in a second, focused study at one end of the gradient. We found that gradients in precipitation, nitrogen deposition, and wind were the most important factors to native richness and exotic species cover across the landscape, while local heterogeneity in bare ground influenced richness and cover at the high deposition/windy, or high-disturbance, end of the gradient. Patterns of native diversity were evaluated across the gradients using non-metric multidimensional scaling, which showed diversity was split into two axes: one strongly correlated to precipitation and the other strongly correlated with disturbance factors. The disturbance factors were also positively associated with exotic grass and forb cover. In total, these results indicate that large-scale patterns in disturbance and exotic species cover negatively affect native annual plant species diversity but native species can also persist due to local heterogeneity.