Soil moisture dynamics reflect the complex interactions of meteorological conditions with soil, vegetation and terrain properties. In this study, intermediate-scale soil moisture estimates from the cosmic-ray neutron sensing (CRNS) method are evaluated for two semiarid ecosystems in the southwestern United States: a mesquite savanna at the Santa Rita Experimental Range (SRER) and a mixed shrubland at the Jornada Experimental Range (JER). Evaluations of the CRNS method are performed for small watersheds instrumented with a distributed sensor network consisting of soil moisture sensor profiles, an eddy covariance tower, and runoff flumes used to close the water balance. We found a very good agreement between the CRNS method and the distributed sensor network (root mean square error (RMSE) of 0.009 and 0.013 m3 m−3 at SRER and JER, respectively) at the hourly timescale over the 19-month study period, primarily due to the inclusion of 5 cm observations of shallow soil moisture. Good agreement was also obtained in soil moisture changes estimated from the CRNS and watershed water balance methods (RMSE of 0.001 and 0.082 m3 m−3 at SRER and JER, respectively), with deviations due to bypassing of the CRNS measurement depth during large rainfall events. Once validated, the CRNS soil moisture estimates were used to investigate hydrological processes at the footprint scale at each site. Through the computation of the water balance, we showed that drier-than-average conditions at SRER promoted plant water uptake from deeper soil layers, while the wetter-than-average period at JER resulted in percolation towards deeper soils. The CRNS measurements were then used to quantify the link between evapotranspiration and soil moisture at a commensurate scale, finding similar predictive relations at both sites that are applicable to other semiarid ecosystems in the southwestern US.