Experiments with the single-column implementation of the Weather Research and Forecasting Model provide a basis for deducing land-atmosphere coupling errors in the model. Coupling occurs both through heat and moisture fluxes through the land-atmosphere interface and roughness sublayer, and turbulent heat, moisture, and momentum fluxes through the atmospheric surface layer. This work primarily addresses the turbulent fluxes, which are parameterized following the Monin-Obukhov similarity theory applied to the atmospheric surface layer. By combining ensemble data assimilation and parameter estimation, the model error can be characterized. Ensemble data assimilation of 2-m temperature and water vapor mixing ratio, and 10-m wind components, forces the model to follow observations during a month-long simulation for a column over the well-instrumented Atmospheric Radiation Measurement (ARM) Central Facility near Lamont, Oklahoma. One-hour errors in predicted observations are systematically small but nonzero, and the systematic errors measure bias as a function of local time of day. Analysis increments for state elements nearby (15 m AGL) can be too small or have the wrong sign, indicating systematically biased covariances and model error. Experiments using the ensemble filter to objectively estimate a parameter controlling the thermal land-atmosphere coupling show that the parameter adapts to offset the model errors, but that the errors cannot be eliminated. Results suggest either structural errors or further parametric errors that may be difficult to estimate. Experiments omitting atypical observations such as soil and flux measurements lead to qualitatively similar deductions, showing the potential for assimilating common in situ observations as an inexpensive framework for deducing and isolating model errors.