The North American monsoon (NAM) contributes roughly half of the annual precipitation in the Chihuahuan Desert from July to September. Relatively frequent, intense storms increase soil moisture and lead to ephemeral runoff. Quantifying these processes, however, is difficult due to the sparse nature of existing observations. This study presents results from a dense network of rain gauges, soil probes, channel flumes, and an eddy covariance tower in a small watershed of the Jornada Experimental Range. Using this network, the temporal and spatial variability of soil moisture conditions and channel runoff were assessed from June 2010 to September 2011. In addition, tower measurements were used to quantify the seasonal, monthly and event-scale changes in land–atmosphere states and fluxes. Results from this study indicate a strong seasonality in water and energy fluxes, with a reduction in the Bowen ratio (B) from winter (B = 14) to summer (B = 3.3). This reduction was tied to higher shallow soil moisture (θ) availability during the summer (θ = 0.040 m3/m3) as compared to winter (θ = 0.004 m3/m3). Four consecutive rainfall–runoff events during the NAM were used to quantify the soil moisture and channel runoff responses and how water availability impacted land–atmosphere fluxes. The network also allowed comparisons of several approaches to estimate evapotranspiration (ET). Using a water balance residual approach, a more accurate ET estimate was obtained when distributed measurements were used, as opposed to single site measurements at the tower. In addition, the spatially-varied soil moisture data yielded a more reasonable daily relation between ET and θ, an important parameterization in many hydrologic models. These analyses illustrate the value of high-resolution sampling in small watersheds to characterize hydrologic processes.