Abstract. Atmospheric transport models are often used to simulate the distribution of greenhouse gases (GHGs). This can be in the context of forward modeling of tracer transport using surface–atmosphere fluxes or flux estimation through inverse modeling, whereby atmospheric tracer measurements are used in combination with simulated transport. In both of these contexts, transport errors can bias the results and should therefore be minimized. Here, we analyze transport uncertainties in the commonly used Weather Research and Forecasting (WRF) model coupled with the greenhouse gas module (WRF-GHG), enabling passive tracer transport simulation of CO2 and CH4. As a mesoscale numerical weather prediction model, WRF's transport is constrained by global meteorological fields via initialization and at the lateral boundaries of the domain of interest. These global fields were generated by assimilating various meteorological data to increase the accuracy of modeled fields. However, in limited-domain models like WRF, the winds in the center of the domain can deviate considerably from these driving fields. As the accuracy of the wind speed and direction is critical to the prediction of tracer transport, maintaining a close link to the observations across the simulation domain is desired. On the other hand, a link that is too close to the global meteorological fields can degrade performance at smaller spatial scales that are better represented by the mesoscale model. In this work, we evaluated the performance of strategies for keeping WRF's meteorology compatible with meteorological observations. To avoid the complexity of assimilating meteorological observations directly, two main strategies of coupling WRF-GHG with ERA5 meteorological reanalysis data were tested over a 2-month-long simulation over the European domain: (a) restarting the model daily with fresh initial conditions (ICs) from ERA5 and (b) nudging the atmospheric winds, temperatures, and moisture to those of ERA5 continuously throughout the simulation period, using WRF's built-in four-dimensional data assimilation (FDDA) in grid-nudging mode. Meteorological variables and simulated mole fractions of CO2 and CH4 were compared against observations to assess the performance of the different strategies. We also compared planetary boundary layer height (PBLH) with radiosonde-derived estimates. Either nudging or daily restarts similarly improved the meteorology and GHG transport in our simulations, with a small advantage of using both methods in combination. However, notable differences in soil moisture were found that accumulated over the course of the simulation when not using frequent restarts. The soil moisture drift had an impact on the simulated PBLH, presumably via changing the Bowen ratio. This is partially mitigated through nudging without requiring daily restarts, although not entirely alleviated. Soil moisture drift did not have a noticeable impact on GHG performance in our case, likely because it was dominated by other errors. However, since the PBLH is critical for accurately simulating GHG transport, we recommend transport model setups that tie soil moisture to observations. Our method of frequently re-initializing simulations with meteorological reanalysis fields proved suitable for this purpose.