This dataset contains ground cover and canopy gap data collected along transects in a long-term experiment (2011-present) of cross-scale interactions (CSIs) at the Jornada Basin LTER site in southern New Mexico, U.S.A. Experimental treatments were initiated in 2013 at 15 experimental blocks, each with 4 treatment plots: plant-scale herbicide of mesquite shrubs, patch-scale connectivity modifiers (ConMods), herbicide + ConMods, control without manipulations. Plant cover was measured along three 25 meter transects in each plot using the line-point intercept (LPI) method. The data table contains cover type occurrences (species or cover type) and status (dead, seedling, etc.) every 25 centimeters along the transect. Canopy gap intercepts were measured along the same transects and the resulting data table contains gap start, end, and interval data. This study is ongoing.