Nighttime vertical profiles of ozone, PM2.5 and PM10 particulate matter, carbon monoxide, temperature, and humidity were collected by a copter-type unmanned aerial vehicle (UAV) over the city of Manaus, Brazil, in central Amazon during the dry season of 2018. The vertical profiles were analyzed to understand the structure of the urban nighttime boundary layer (NBL) and pollution within it. The ozone concentration, temperature, and humidity had an inflection between 225 and 350 m on most nights, representing the top of the urban NBL. The profile of carbon monoxide concentration correlated well with the local evening vehicular congestion of a modern transportation fleet, providing insight into the surface-atmosphere dynamics. In contrast, events of elevated PM2.5 and PM10 concentrations were not explained well by local urban emissions, but rather by back trajectories that intersected regional biomass burning. These results highlight the potential of the emerging technologies of sensor payloads on UAVs to provide new constraints and insights for understanding the pollution dynamics in nighttime boundary layers in urban regions.