A severe marine heatwave was observed in the southwest Atlantic in summer 2013-14 coinciding with an intense drought over southeast South America. Over land it led to water shortages in São Paulo, the world’s fourth most populated city, and tripled the dengue fever cases with fatalities. Similarly, ocean heatwaves can severely impact local ecosystems. The effects of the 2013-14 event for the South Atlantic marine biology is yet to be quantified, although a significant drop in the chlorophyll suggests a reduction in primary production and fishery in the region. This study investigates the mechanisms that triggered the marine heatwave in the southwest Atlantic. We found that the ocean heatwave was caused by the same mechanism that triggered the drought in southeast South America, i.e. atmospheric blocking events that persisted almost the entire summer over the region. The atmospheric blocking was triggered by convection in the eastern Indian Ocean associated with Madden-Julian Oscillation. The atmospheric blocking-related anticyclone inhibited cloud cover off southeast Brazil coast and increased shortwave radiation as well as weakened surface winds and reduced ocean heat loss thus establishing the marine heatwave in the region. We further show that the atmospheric blocking explains approximately 60% of the marine heatwave events in the southwestern Atlantic. An increase in frequency, duration, intensity and extension of marine heatwave events is seen over the satellite period 1982–2016. By understanding when and how these events form we can start to predict them and provide forewarning to local industries and communities.