The recent development of the non-invasive cosmic-ray soil moisture sensing technique fills the gap between point-scale soil moisture measurements and regional-scale soil moisture measurements by remote sensing. A cosmic-ray probe measures soil moisture for a footprint with a diameter of ∼ 600 m (at sea level) and with an effective measurement depth between 12 and 76 cm, depending on the soil humidity. In this study, it was tested whether neutron counts also allow correcting for a systematic error in the model forcings. A lack of water management data often causes systematic input errors to land surface models. Here, the assimilation procedure was tested for an irrigated corn field (Heihe Watershed Allied Telemetry Experimental Research-HiWATER, 2012) where no irrigation data were available as model input although for the area a significant amount of water was irrigated. In the study, the measured cosmic-ray neutron counts and Moderate-Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) products were jointly assimilated into the Community Land Model (CLM) with the local ensemble transform Kalman filter. Different data assimilation scenarios were evaluated, with assimilation of LST and/or cosmic-ray neutron counts, and possibly parameter estimation of leaf area index (LAI). The results show that the direct assimilation of cosmic-ray neutron counts can improve the soil moisture and evapotranspiration (ET) estimation significantly, correcting for lack of information on irrigation amounts. The joint assimilation of neutron counts and LST could improve further the ET estimation, but the information content of neutron counts exceeded the one of LST. Additional improvement was achieved by calibrating LAI, which after calibration was also closer to independent field measurements. It was concluded that assimilation of neutron counts was useful for ET and soil moisture estimation even if the model has a systematic bias like neglecting irrigation. However, also the assimilation of LST helped to correct the systematic model bias introduced by neglecting irrigation and LST could be used to update soil moisture with state augmentation.