Accurate simulation of planetary boundary layer height (PBLH) is key to greenhouse gas emission estimation, air quality prediction and weather forecasting. This manuscript describes an extensive performance assessment of several Weather Research and Forecasting (WRF) model configurations where novel observations from ceilometers, surface stations and a flux tower were used to study their ability to reproduce planetary boundary layer heights (PBLH) and the impact that the urban heat island (UHI) has on the modeled PBLHs in the greater Washington, D.C. area. In addition, CO2 measurements at two urban towers were compared to tracer transport simulations. The ensemble of models used 4 PBL parameterizations, 2 sources of initial and boundary conditions and 1 configuration including the building energy parameterization (BEP) urban canopy model. Results have shown low biases over the whole domain and period for wind speed, wind direction and temperature with no drastic differences between meteorological drivers. We find that PBLH errors are mostly positively correlated with sensible heat flux errors, and that modeled positive UHI intensities are associated with deeper modeled PBLs over the urban areas. In addition, we find that modeled PBLHs are typically biased low during nighttime for most of the configurations with the exception of those using the MYNN parametrization and that these biases directly translate to tracer biases. Overall, the configurations using MYNN scheme performed the best, reproducing the PBLH and CO2 molar fractions reasonably well during all hours, thus opening the door to future nighttime inverse modeling.