The Hadley Centre coupled climate–carbon cycle model (HadCM3LC) predicts loss of the Amazon rainforest in response to future anthropogenic greenhouse gas emissions. In this study, the atmospheric component of HadCM3LC is used to assess the role of simulated changes in mid-twenty-first century sea surface temperature (SST) in Amazon Basin climate change. When the full HadCM3LC SST anomalies (SSTAs) are used, the atmosphere model reproduces the Amazon Basin climate change exhibited by HadCM3LC, including much of the reduction in Amazon Basin rainfall. This rainfall change is shown to be the combined effect of SSTAs in both the tropical Atlantic and the Pacific, with roughly equal contributions from each basin. The greatest rainfall reduction occurs from May to October, outside of the mature South American monsoon (SAM) season. This dry season response is the combined effect of a more rapid warming of the tropical North Atlantic relative to the south, and warm SSTAs in the tropical east Pacific. Conversely, a weak enhancement of mature SAM season rainfall in response to Atlantic SST change is suppressed by the atmospheric response to Pacific SST. This net wet season response is sufficient to prevent dry season soil moisture deficits from being recharged through the SAM season, leading to a perennial soil moisture reduction and an associated 30% reduction in annual Amazon Basin net primary productivity (NPP). A further 23% NPP reduction occurs in response to a 3.5°C warmer air temperature associated with a global mean SST warming.