The Program for Research on Oxidants: Photochemistry, Emissions, and Transport (PROPHET) has conducted intensive observations of atmospheric chemistry and the nocturnal boundary layer at the University of Michigan Biological Station (UMBS) during July and August of 1998, 2000, and 2001. There has been a continuing interest in nighttime atmospheric chemistry during the PROPHET chemistry intensives. Continuous chemical measurements are made on a 30-meter tower within a mixed hardwood forest. Additionally chemical profiles are made using a small aircraft to complement/support the tower measurements. For the past two summers, 2000 and 2001, an Integrated Sounding System (ISS) from NCAR (National Center for Atmospheric Research) has been deployed to provide detailed measurements of boundary layer structure. The ISS consists of a 915 MHz wind profiler, RASS (radio acoustic sounding system), a 10-meter meteorological tower, and the capability to obtain atmospheric profiles using rawinsondes and tethered rawinsondes. Virtual temperature profiles are produced every half hour using RASS. A limitation of RASS is that the first range gate is at 120-m, which is too high to follow the early development of the nocturnal boundary layer. For this reason, rawinsondes and tethered rawinsondes were used to gather atmospheric profiles of temperature and relative humidity from the surface up to 250-m. In this paper we will demonstrate the effects that the nocturnal boundary layer has on the nighttime atmospheric chemistry at the PROPHET site. Distinct synoptic transport from the continental-polar air mass to the north of the PROPHET site and from the maritime-subtropical air mass to the south of the site were studied. The nocturnal boundary layer was studied by launching tethered rawinsondes every half-hour, while chemical measurements of NOx, isoprene, and other hydrocarbons were measured during the atmospheric profiling period.