More than half of the world's current population resides in urban areas, and cities account for roughly three-quarters of the total greenhouse gas emissions. Current and future trends in urbanization will have significant impacts on global climate. However, our collective understanding of the climate of urban areas remains deficient, which is mainly related to significant knowledge gaps in observations. The New York City Summer Heat Campaign was initiated to address some of these critical knowledge gaps. As part of the campaign the urban boundary layer over New York City was continuously monitored during July 2016, a period that witnessed three heatwave events. Surface weather stations and indoor sensors were also used to characterize the urban heat island intensity. Our results reveal that during the month, the urban heat island intensity was nearly twice compared to the decadal average. During the heatwave episodes, urban heat island intensities as high as 10 °C were observed. The thermal profiles indicate elevated temperatures in much of the boundary layer between 800–2500 m during the heatwave episodes. The profiles indicate a complex thermal structure and high intra-city variability. Thermal internal boundary layer was observed in neighborhoods populated by tall buildings. Overall the high-pressure system during the heatwave episodes acted as a thermal block and much of the heat generated in the urban surface layer remained within the boundary layer, thereby amplifying the near surface air temperature.