© 2014 Society for Ecological Restoration. Invasion by exotic annual species is increasingly impacting Southern California arid lands, altering ecosystem processes and plant community composition. With climate change, the Southwestern United States is expected to experience increasingly variable rainfall. Larger rainfall events could facilitate invasion by exotic species that can capitalize on high resource conditions. Exotic annual species also have dense shallow root systems that could create positive feedbacks to further invasion by increasing soil organic matter and water holding capacity. Alternatively, fine root inputs could create negative feedbacks to exotic plant growth if they stimulate microbial nutrient immobilization. The dual influences of rainfall regime and fine root inputs on species performance were evaluated in an experiment where native and exotic species were grown individually and in combination under varying watering regimes (large infrequent or small frequent pulses, holding total rainfall constant) and root additions (with or without sterilized exotic roots). Mean soil moisture increased with larger infrequent watering events, and also with root addition. Plant growth (both native and exotic) increased with larger watering events, but declined with root addition. Exotic species growth declined more than native species growth with root additions. Mechanistically, root addition lowered inorganic nitrogen (N) availability, and microbial N immobilization increased with soil moisture content. Together these results show that increased fine root production promotes negative feedbacks to growth of exotic species via microbial N immobilization, especially under conditions of high soil moisture. Further, our results suggest that organic carbon additions are a potentially effective strategy for suppressing growth of problematic desert invaders.