Multi-year climatic periods are expected to increase with global change, yet long-term data are often insufficient to document factors leading to ecological responses. We used a suite of long-term datasets (1993-2010) to examine the processes underlying different relationships between aboveground net primary production (ANPP) and precipitation in wet and dry rainfall periods in shrublands and grasslands in the Chihuahuan Desert. We hypothesized that trends in ANPP can be explained by different processes associated with their dominant grasses [Bouteloua eriopoda (grasslands); Sporobolus flexuosus (shrublands)] and with ecosystem properties that influence soil water dynamics with feedbacks to ANPP. We compared datasets on recruitment and growth for 7 years with no trend in precipitation followed by a 4-year drought and 5 consecutive wet years. We integrated these data in a simulation model to examine the importance of positive feedbacks. In grasslands, ANPP was linearly related to precipitation regardless of rainfall period, primarily as a result of stolon recruitment by B. eriopoda. A lag in responses suggests the importance of legacies associated with stolon density. In shrublands, ANPP was only related to rainfall in the wet period when it increased nonlinearly as the number of wet years increased. Seed availability increased in the first wet year, and seedling establishment occurred 2-4 years later. Increases in biomass, litter and simulated transpiration beginning in the third year corresponded with increases in ANPP. Understanding the processes underlying ecosystem dynamics in multi-year dry or wet periods is expected to improve predictions under directional increases or decreases in rainfall.