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Significant knowledge gaps exist in our understanding of urban boundary layer processes, particularly the hygrothermal state. The earth system community has successfully used microwave radiometers for several decades. However, the applicability in complex urban environments has never been adequately tested. Here, observations from a microwave radiometer are compared to radiosonde readings in a densely urbanized site in Houston, Texas. The site was influenced by both an urban heat island and the sea breeze phenomenon. The analysis showed significant disagreement between the virtual potential temperature predicted by the microwave radiometer and the radiosonde for all periods within the boundary layer. However, the values were reasonably comparable above the boundary layer. The microwave radiometer incorrectly predicted an inversion layer instead of a mixed layer during convective periods. The microwave radiometer measurements deviated from the radiosonde measurements throughout the lower troposphere for the relative humidity.