This data release presents data used for analyzing spatial and temporal differences in soil surface roughness within selected biocrust communities. These records were collected by ground-based lidar for 121, 1m x 3m soil plots with biological soil crusts (biocrusts). Roughness was estimated from 5 mm resolution data (CloudCompare v. 2.10.2, 2019) for two Great Basin Desert sites (UTTR-1; UTTR-2) in December 2015 and one Chihuahuan Desert site (JER) in February 2016. Data were again collected in June 2018 for UTTR-1 and UTTR-2. Additional field and laboratory data were included within this study to understand differences in soil surface roughness between UTTR and JER as well as between the 2016 and 2018 surveys at UTTR. The associated manuscript (see Larger Work Citation) reports that soil surfaces at the UTTR are significantly rougher than JER for undisturbed biocrust but not necessarily for disturbed biocrust. Additionaly, discuss that once biocrust is disturbed, soil surface roughness can increase with biocrust recovery. These data can be further used to represent surface conditions at the time of collection at individual soil plots within both study areas, providing further information on spatial and temporal variability in roughness as well as other field and laboratory parameters included in this release.