Insights into the effects of climatic changes on primary metabolism in plants will enhance our understanding of ecosystem response to global climate change. In a greenhouse experiment, we studied the impact of total annual rainfall, intermittent wet and dry periods, and increased soil and air temperature (+3 °C) on an annual C3 grass, Avena barbata, dominant in many California and Mediterranean grasslands. In order to gain a mechanistic understanding of plant response, analyses were carried out at scales ranging from the leaf (gene expression and enzyme activity) to the whole plant (biomass and phenology). Plant gene expression was more responsive to short-term changes in water availability (wet vs. dry periods) than to differences in cumulative rainfall. The effect of elevated temperature depended on total rainfall: flowering started earlier in high vs. low temperature under high rainfall, but not under low rainfall. Gene expression indicative of advanced development could be measured in leaves several weeks before flowering, linking gene expression to the phenological impact of altered climate. Given these responses of a dominant annual grass to manipulation of rain and temperature, we suggest that the impact of increased temperature on California annual grasslands will vary between wet and dry years. In wet years, biomass production will increase and flowering will occur earlier compared with dry years. Leaf transcript abundance analyses provided insights into the mechanisms of plant response to warming and altered precipitation patterns.