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Deserts are characterized by low productivity and substantial unvegetated space, which is often covered by soil microbial crust communities. Microbial crusts are important for nitrogen fixation, soil stabilization and water infiltration, but their role in ecosystem production is not well understood. This study addresses the following questions: what are the CO2 exchange responses of crusts to pulses of water, does the contribution of crusts to ecosystem flux differ from the soil respiratory flux, and is this contribution pulse size dependent? Following water application to crusts and soils, CO2 exchange was measured and respiration was partitioned through mixing model analysis of Keeling plots across treatments. Following small precipitation pulse sizes, crusts contributed 80% of soil-level CO2 fluxes to the atmosphere. However, following a large pulse event, roots and soil microbes contributed nearly 100% of the soil-level flux. Rainfall events in southern Arizona are dominated by small pulse sizes, suggesting that crusts may frequently contribute to ecosystem production. Carbon cycle studies of and land systems should consider crusts as important contributors because of their dynamic responses to different pulse sizes as compared to the remaining ecosystem components.