Soil moisture status in the root zone is an important component of the water cycle at all spatial scales (e.g., point, field, catchment, watershed, and region). In this study, the spatio-temporal evolution of root zone soil moisture of the Walnut Gulch Experimental Watershed (WGEW) in Arizona was investigated during the Soil Moisture Experiment 2004 (SMEX04). Root zone soil moisture was estimated via assimilation of aircraft-based remotely sensed surface soil moisture into a distributed Soil-Water-Atmosphere-Plant (SWAP) model. An ensemble square root filter (EnSRF) based on a Kalman filtering scheme was used for assimilating the aircraft-based soil moisture observations at a spatial resolution of 800 m x 800 m. The SWAP model inputs were derived from the SSURGO soil database, LAI (Leaf Area Index) data from SMEX04 database, and data from meteorological stations/rain gauges at the WGEW. Model predictions are presented in terms of temporal evolution of soil moisture probability density function at various depths across the WGEW. The assimilation of the remotely sensed surface soil moisture observations had limited influence on the profile soil moisture. More specifically, root zone soil moisture depended mostly on the soil type. Modeled soil moisture profile estimates were compared to field measurements made periodically during the experiment at the ground based soil moisture stations in the watershed. Comparisons showed that the ground-based soil moisture observations at various depths were within +/- 1 standard deviation of the modeled profile soil moisture. Density plots of root zone soil moisture at various depths in the WGEW exhibited multi-modal variations due to the uneven distribution of precipitation and the heterogeneity of soil types and soil layers across the watershed.