In semi-arid savannas, dominance of intercanopy space by annual or perennial grasses may alter partitioning of ecosystem water and carbon fluxes and affect ecosystem water use efficiency (WUEe), the ratio of net ecosystem carbon dioxide exchange (NEE) to evapotranspiration (ET). To establish if these contrasting growth habits changed controls to WUEe, we tracked volumetric soil moisture (θ25cm), ET and transpiration (T), NEE and its constituent ecosystem respiration (Reco) and gross ecosystem photosynthesis (GEP) fluxes, and community water use efficiency (WUEc = GEP : T) in annual-dominated and bunchgrass-dominated plots in a southern Arizona, United States, savanna. Annual and bunchgrass plots had similar θ25cm, ET, and T, suggesting the similarity in ET was due to higher soil evaporation in annual plots. Seasonal NEE was delayed and lower in annual plots compared with that in bunchgrass plots, owing to higher Reco in annual plots. Transpiration, GEP, and Reco in both vegetation types increased following late-season rain, indicating similar late-season phenological constraint. WUEe was lower in annual plots, but with similar WUEc between plot types. These results suggest that differences in annual plant biomass allocation and plot-level leaf area distribution increased proportional soil evaporation and aboveground Reco contributions, reducing plot-level WUEe, not lowering plant WUE typical of arid-land annuals. Lower plot-level WUEe suggests that any increase in annual plant dominance would increase interannual variation of productivity in savanna intercanopy spaces, which could enhance the negative effects of predicted higher temperatures, greater aridity, and larger and more widely spaced storms on arid-land watershed processes. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.