The behavior of ecohydrological systems can be assessed from the interactions between ecosystem states and atmospheric fluxes, including water, carbon and energy dynamics. In this study, we present progress on implementing automatic and continuous measurements of soil temperature and soil moisture within the estimated footprints of eddy covariance towers at two shrubland sites in the American Southwest. The two sites are mixed shrubland in southern New Mexico at the Jornada Experimental Range and a desert savanna in southern Arizona at the Santa Rita Experimental Range. Both sites feature a high temporal variability in vegetation greenness due to rainfall seasonality induced by the North American monsoon. In addition, woody plant encroachment at each site has led to a mosaic of different herbaceous and shrub species. We expect the plant cover heterogeneity to significantly impact the eddy covariance flux measurements and that this effect cannot be adequately captured by surface measurements at the tower. Here, we present estimates of the eddy covariance footprint in each shrubland ecosystem and the sensor network design utilized for continuous measurements within each footprint. These designs relied on high--resolution elevation and vegetation classification maps derived from manned and unmanned aerial vehicles. Ultimately, this study will help characterize the ecohydrological dynamics of these shrubland systems as well as the suitability of the eddy covariance method for heterogeneous landscapes.