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Rainfall variability is a key driver of ecosystem structure and function in grasslands worldwide. Changes in rainfall patterns predicted by global climate models for the central United States are expected to cause lower and increasingly variable soil water availability, which may impact net primary production and plant species composition in native Great Plains grasslands. We experimentally altered the timing and quantity of growing season rainfall inputs by lengthening inter-rainfall dry intervals by 50%, reducing rainfall quantities by 30%, or both, compared to the ambient rainfall regime in a native tallgrass prairie ecosystem in northeastern Kansas. Over three growing seasons, increased rainfall variability caused by altered rainfall timing with no change in total rainfall quantity led to lower and more variable soil water content (0-30 cm depth), a similar to10% reduction in aboveground net primary productivity (ANPP), increased root to shoot ratios, and greater canopy photon flux density at 30 cm above the soil surface. Lower total ANPP primarily resulted from reduced growth, biomass and flowering of subdominant warm-season C-4 grasses while productivity of the dominant C-4 grass Andropogon gerardii was relatively unresponsive. In general, vegetation responses to increased soil water content variability were at least equal to those caused by imposing a 30% reduction in rainfall quantity without altering the timing of rainfall inputs. Reduced ANPP most likely resulted from direct effects of soil moisture deficits on root activity, plant water status, and photosynthesis. Altered rainfall regimes are likely to be an important element of climate change scenarios in this grassland, and the nature of interactions with other climate change elements remains a significant challenge for predicting ecosystem responses to climate change.