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Ongoing, widespread increases in woody plant abundance in historical grasslands and savannas (woody encroachment) likely will interact with future precipitation variability to influence seasonal patterns of carbon cycling in water-limited regions. To characterize the effects of woody encroachment on the sensitivity of ecosystem carbon exchange to seasonal rainfall in a semi-arid riparian setting we used flux-duration analysis to compare 2003-growing season NEE data from a riparian grassland and shrubland. Though less seasonally variable than the grassland, shrubland NEE was more responsive to monsoon rains than anticipated. During the 2004-growing season we measured leaf gas exchange and collected leaf tissue for delta C-13 and nitrogen content analysis periodically among three size classes of the dominant woody-plant, Prosopis velutina and the dominant understory species, Sporobolus wrightii, a C-4 bunchgrass, present at the shrubland. We observed size-class and plant functional type independent patterns of seasonal plant performance consistent with greater-than-anticipated sensitivity of NEE in the shrubland. This research highlights the complex interaction between growing-season precipitation, plant-available alluvial groundwater and woody plant abundance governing ecosystem carbon balance in this semi-arid watershed.