A number of studies have used time series of air temperature and specific humidity observations to estimate turbulent heat fluxes. These studies require the specification of surface roughness lengths for heat and momentum (that are directly related to the neutral bulk heat transfer coefficient CHN) and/or ground heat flux, which are often unavailable. In this study, sequences of air temperature and specific humidity are assimilated into an atmospheric boundary layer model within a variational data assimilation (VDA) framework to estimate CHN, evaporative fraction (EF), turbulent heat fluxes, and atmospheric boundary layer (ABL) height, potential temperature, and humidity. The developed VDA approach needs neither the surface roughness parameterization (as it is optimized by the VDA approach) nor ground heat flux measurements. The VDA approach is tested over the First International Satellite Land Surface Climatology Project Field Experiment (FIFE) site in the summers of 1987 and 1988. The results indicate that the estimated sensible and latent heat fluxes agree fairly well with the corresponding measurements. For FIFE 1987 (1988), the daily sensible and latent heat fluxes estimates have a root-mean-square error of 25.72 W m−2 (27.77 W m−2) and 53.63 W m−2 (48.22 W m−2), respectively. In addition, the ABL height, specific humidity, and potential temperature estimates from the VDA system are in good agreement with those inferred from the radiosondes both in terms of magnitude and diurnal trend.