Soil moisture distribution emerges as a key link between hydrologic and ecologic processes in semiarid grassland and shrubland, as it influences evapotranspiration, respiration, and assimilation. In support, we present three years of data (2002–2004) collected from a semiarid grassland and shrubland within the Sevilleta National Wildlife Refuge of central New Mexico; the two sites are separated by about 5 km. Instrumentation includes an eddy covariance tower and typical micrometeorological devices at both locations. Additionally, the grassland site features six soil moisture profiles and the shrubland site features four soil moisture profiles, with the maximum depth at 52.5 cm. At both sites, most rain falls during the warm season, but large storms do occur at other times of the year, e.g., spring of 2004. Soil moisture pulses at 2.5 cm follow almost all rain events, whereas only four pulses in the 3-year record are observed at 52.5 cm in the grassland and two in the shrubland; these deeper pulses follow large precipitation events or a series of smaller events. The daily times series of evapotranspiration (ET) is similar between the grassland and shrubland, supporting the results of Kurc and Small (2004). ET variations largely reflect changes in the soil moisture at 2.5 cm. In contrast, though the daily time series of net ecosystem exchange (NEE) at both sites covary, the magnitudes of peaks in net negative ecosystem exchange (NEE−) and net positive ecosystem exchange (NEE+) are over twice the magnitude at grassland than at the shrubland. Furthermore, pulses associated with NEE− peaks last much longer than ET pulses, of the order of 1–2 months, without any particular adherence to the climatologically defined rainy season. These NEE− pulses reflect changes in deeper soil moisture, i.e., 52.5 cm at the grassland and 37.5 cm at the shrubland. Finally, evidence of soil moisture driven respiration is found throughout the NEE time series, with spikes of NEE+ following most rain events; however, longer periods of NEE+ also occur during relatively dry periods. Modeled assimilation suggests that the relationship between assimilation and soil moisture is strongest at depths at least 30 cm below the surface.