This study investigates the impact of surface heterogeneity on the timing of the morning transitions observed during the 1999 Southern Oxidants Study Nashville/Middle Tennessee Intensive (SOS99N). The end of the morning transition occurs at a measurement site located in the Cumberland River Valley approximately 8 km northeast of downtown Nashville, on average, 1.25 h earlier than at three rural sites surrounding Nashville. This study shows that the early morning behavior of the boundary layers observed at the river valley site is dominated by local terrain features, whereas a previous study showed that the afternoon boundary layers observed at this site are more strongly influenced by its urban characteristics. Profiles of backscatter intensity recorded by monostatic sodars and Doppler wind profilers are analyzed to provide the evolution of boundary layer depth on days when a nocturnal inversion formed. These measurements indicate that the early morning growth rate of the convective boundary layer was faster, on average, at the river valley site in Nashville than at a rural, non-river valley site where similar measurements were made (125 m h-1 versus 73 m h-1 from 0600 to 0800 h CST). A comparison of temperature profiles measured with radio acoustic sounding systems indicates that low-level stability resulting from the nocturnal boundary layer had a stronger influence than surface energetics on the observed variations in boundary layer depth and morning transition end times. A single case study is shown to demonstrate the potential impact of the morning transition on gas phase chemistry measurements collected at a rural site. Case study and diurnally averaged time series show how surface-layer humidity can be an effective tracer for diagnosing the end of the morning transition.